This line looks wrong:

for (int j = s[i].length()-1; i >= 0; i--)

It should be:

for (int j = s[i].length()-1; j >= 0; j--)

In other words: the indexes in the inner loop are mistaken, they should be using j instead of i. As a side comment - here's a simpler way to reverse a string:

reverse = new StringBuilder(s[i]).reverse().toString();

Stream

The Answer by Elliott Frisch is correct and robust, and should be accepted.

In addition, for fun, here is a version of that code using streams rather than the conventional for loop. I am not claiming this is better.

I do not know of a way for a stream of an array to affect that array. So instead here I make and return a fresh array.

public static String[] reverse( String[] array ) {
    Objects.requireNonNull( array , "Received null argument where an array of `String` was expected. Message # b5c03336-4b9e-4735-a054-16e43aac059e.") ;
    
    Stream< String > stream = Arrays.stream( array ) ;
    String[] result =
            stream
            .map( ( String s ) -> new StringBuilder( s ).reverse().toString() )
            .toArray(String[]::new) 
    ;
    
    return result ;
}

Usage.

    String arr[] = { "abc" , "def" , "mask" } ;
    String arr2[] = Ideone.reverse( arr ) ;
    
    System.out.println( Arrays.toString( arr ) ) ;
    System.out.println( Arrays.toString( arr2 ) ) ;

See that code run live at IdeOne.com.

[abc, def, mask]

[cba, fed, ksam]

You can transform your string into StringBuilder and it had reverse method. And its always better to use foreach rather than for, until there is actual need.

public String[] reverseString(String[] words) {
    String[] t = new String[words.length];
    for (String wordTemp : words) {
      StringBuilder sb = new StringBuilder(wordTemp);
      t[i] = sb.reverse().toString();   
    }
    return t;
}

Alternate approach :-

public  String[]  reverseString(String[] words)
{
    String[] t=new String[words.length];

    for(int i=0;i<words.length;i++)
    {   
        //added for setting elemennt as emptyString instead of null
        t[i] = "";
        for(int j=words[i].length()-1;j>=0;j--)
        {
            t[i]+=words[i].substring(j,j+1);
        }
    }

    //using loop
    for(int i=0;i<words.length;i++)
    {
         System.out.println(t[i]);
    }
    //using Arrays Method
    System.out.println(Arrays.toString(t));
    return t;
}