You haven't created three different empty lists. You've created one empty list, and then created a new list with three references to that same empty list. To fix the problem use this code instead:

listy = [[] for i in range(3)]

Running your example code now gives the result you probably expected:

>>> listy = [[] for i in range(3)]
>>> listy[1] = [1,2]
>>> listy
[[], [1, 2], []]
>>> listy[1].append(3)
>>> listy
[[], [1, 2, 3], []]
>>> listy[2].append(1)
>>> listy
[[], [1, 2, 3], [1]]

You can iterate through the items of the lists and then add them to your masterlist:

a = [[1,2,3],
     [1,2,3]]   
b = [[4,5,6],
     [4,5,6]]

masterlist = []

for aa,bb in zip(a,b):                 # loop over lists
    for itema, itemb in zip(aa,bb):    # loop over items in list
        masterlist = masterlist + [[itema, itemb]]

output:

[[1, 4], [2, 5], [3, 6], [1, 4], [2, 5], [3, 6]]

You do not "declare" arrays or anything else in python. You simply assign to a (new) variable. If you want a multidimensional array, simply add a new array as an array element.

arr = []
arr.append([])
arr[0].append('aa1')
arr[0].append('aa2')

or

arr = []
arr.append(['aa1', 'aa2'])

I would suggest first creating the inner array, and then appending it to outer array as a whole, like this:

trends = []
for file in files:
    file_result = []
    with open(file) as csv_file:
        csv_reader = csv.reader(csv_file, delimiter=',') 
        next(csv_reader) # To skip the header
        for row in csv_reader:
            file_result.append(row[1])
    trends.append(file_result)

This way you don't need to keep the counters at all and your code will be easier to read.

You also don't need to close the file if you are using context manager (with statement)

Here's one way using set and itertools.chain:

from itertools import chain

b_set = set(chain.from_iterable(b))
res = b + [[i] for i in a if i not in b_set]

print(res)

[[231, 220, 222, 244], [200, 201], [202]]