In a normal C program running on a modern OS, file access is buffered twice (or more when you count buffers like the buffer in your drive). One buffer is implemented in the FILE structure and the other is implemented in the kernel.

Often, the FILE structure buffers the content in a buffer inside of your program. When you write something to a buffered file, the content is keep in the buffer, inside of the running program. It is written to the OS when the buffer is full and, when the buffering mode is line buffered, at the end of a line. This data is written to the OS by a syscall, for example write(). The buffer is there because a syscall requires a context switch from the user program to the kernel, this is relatively expensive (slow), the buffer is here to reduce the number of syscalls. You could also use the syscalls from your program directly without the stdio functions, however, this functions are less portable and more complex to handle. A fflush(stdout) checks if there are any data in the buffer that should be written and if so, the underlying syscall is used to write the data to the OS.

When the syscall returns, the data is in your kernel. But modern operating systems buffer this data as well. This is used to reduce the number of disk writes, reduce latency and other things. This buffer is completely independent of the FILE buffer inside your program.

Note that this does not apply to all systems. For example microcontroller environments may provide some stdio.h functions that write directly to a UART, without any buffer, neither inside FILE nor any (probably non-existent) OS.

To see what fflush() does to a running program, compare this programs:

int main(void)
{
  fputs("s",stdout);
  fputs("e",stderr);
}

and

int main(void)
{
  fputs("s",stdout);
  fflush(stdout);
  fputs("e",stderr);
}

On Linux, stderr is not buffered by default, so fputs("e",stderr); will print the data immediately. On the other hand, fputs("s",stdout); is line buffered by default on Linux so the data is not printed immediately. This causes the first program to output es and not se, but the second one outputs se.

You can change the buffer modes with setvbuf()

The answer to this is that fflush(stream) is only formally defined for output streams, so fflush(stdout) is OK, but fflush(stdin) is not.

The purpose of fflush(stream) is to make the operating system flush any buffers to the underlying file. For an example of a legitimate use, students often have problems like “my prompt doesn't appear!” if they do something like:

printf("Enter a number: ");

However, they find that this works just fine:

printf("Enter a number:\n");

Of course, they don't want a newline after their prompt, so they have a bit of a problem.

The reason for this is that the output to stdout is buffered by the OS and the default behavior is (often) only to actually write the output to the terminal when a newline is encountered. Adding an fflush(stdout) after the printf() solves the problem:

printf("Enter a number: ");
fflush(stdout);

Now, working by analogy, people often think that fflush(stdin) should discard any unused input, but if you think about it a little bit that doesn't make much sense. What does it mean to “flush” an input buffer? Where is it “flushed” to? If you flush an output buffer, the output is sent to the underlying file or the terminal, where it would eventually wind up anyway, but where would input “eventually end up anyway”? There's no way of knowing! What should the behavior be if the input stream data comes from a file or a pipe or a socket? It isn't at all clear for input streams what the behavior of fflush() should be, but it's very clear for output streams in all cases. Hence, fflush() is only defined for output streams.

The reason why the erroneous use of fflush(stdin) became commonplace is that, many years ago, a few operating systems did implement a scheme where it worked as many people expected, discarding unused input. Microsoft DOS is a good example. Surprisingly, modern versions of Linux also implement fflush() for input streams.

The right thing to do with “extra” unwanted terminal input is simply to read it and do nothing with it. This is almost as easy as calling fflush(stdin), works everywhere, and doesn't rely on formally undefined behavior.

The C standard says:

If stream points to an output stream or an update stream in which the most recent operation was not input, the fflush function causes any unwritten data for that stream to be delivered to the host environment to be written to the file; otherwise, the behavior is undefined.

POSIX says (also explicitly defers to C standard):

If stream points to an output stream or an update stream in which the most recent operation was not input, fflush() shall cause any unwritten data for that stream to be written to the file, ...

But the Linux manpage says:

For output streams, fflush() forces a write of all user-space buffered data for the given output or update stream via the stream's underlying write function. For input streams, fflush() discards any buffered data that has been fetched from the underlying file, but has not been consumed by the application. The open status of the stream is unaffected.

It's a little hard to say what "can be problems with" (excessive?) use of fflush. All kinds of things can be, or become, problems, depending on your goals and approaches. Probably a better way to look at this is what the intent of fflush is.

The first thing to consider is that fflush is defined only on output streams. An output stream collects "things to write to a file" into a large(ish) buffer, and then writes that buffer to the file. The point of this collecting-up-and-writing-later is to improve speed/efficiency, in two ways:

• On modern OSes, there's some penalty for crossing the user/kernel protection boundary (the system has to change some protection information in the CPU, etc). If you make a large number of OS-level write calls, you pay that penalty for each one. If you collect up, say, 8192 or so individual writes into one large buffer and then make one call, you remove most of that overhead.
• On many modern OSes, each OS write call will try to optimize file performance in some way, e.g., by discovering that you've extended a short file to a longer one, and it would be good to move the disk block from point A on the disk to point B on the disk, so that the longer data can fit contiguously. (On older OSes, this is a separate "defragmentation" step you might run manually. You can think of this as the modern OS doing dynamic, instantaneous defragmentation.) If you were to write, say, 500 bytes, and then another 200, and then 700, and so on, it will do a lot of this work; but if you make one big call with, say, 8192 bytes, the OS can allocate a large block once, and put everything there and not have to re-defragment later.

So, the folks who provide your C library and its stdio stream implementation do whatever is appropriate on your OS to find a "reasonably optimal" block size, and to collect up all output into chunk of that size. (The numbers 4096, 8192, 16384, and 65536 often, today, tend to be good ones, but it really depends on the OS, and sometimes the underlying file system as well. Note that "bigger" is not always "better": streaming data in chunks of four gigabytes at a time will probably perform worse than doing it in chunks of 64 Kbytes, for instance.)

But this creates a problem. Suppose you're writing to a file, such as a log file with date-and-time stamps and messages, and your code is going to keep writing to that file later, but right now, it wants to suspend for a while and let a log-analyzer read the current contents of the log file. One option is to use fclose to close the log file, then fopen to open it again in order to append more data later. It's more efficient, though, to push any pending log messages to the underlying OS file, but keep the file open. That's what fflush does.

Buffering also creates another problem. Suppose your code has some bug, and it sometimes crashes but you're not sure if it's about to crash. And suppose you've written something and it's very important that this data get out to the underlying file system. You can call fflush to push the data through to the OS, before calling your potentially-bad code that might crash. (Sometimes this is good for debugging.)

Or, suppose you're on a Unix-like system, and have a fork system call. This call duplicates the entire user-space (makes a clone of the original process). The stdio buffers are in user space, so the clone has the same buffered-up-but-not-yet-written data that the original process had, at the time of the fork call. Here again, one way to solve the problem is to use fflush to push buffered data out just before doing the fork. If everything is out before the fork, there's nothing to duplicate; the fresh clone won't ever attempt to write the buffered-up data, as it no longer exists.

The more fflush-es you add, the more you're defeating the original idea of collecting up large chunks of data. That is, you are making a tradeoff: large chunks are more efficient, but are causing some other problem, so you make the decision: "be less efficient here, to solve a problem more important than mere efficiency". You call fflush.

Sometimes the problem is simply "debug the software". In that case, instead of repeatedly calling fflush, you can use functions like setbuf and setvbuf to alter the buffering behavior of a stdio stream. This is more convenient (fewer, or even no, code changes required—you can control the set-buffering call with a flag) than adding a lot of fflush calls, so that could be considered a "problem with use (or excessive-use) of fflush".