Randint does not generate random numbers the second time I use it

The problem is that you are not creating new arrays on each call to gerar_matriz() - what you do is add new numbers to the end of each already existing line.

And at the time of printing the lines, you used a fixed size of 3, so you always see the first three elements of the line.Just change your internal print for to see what's going on:

    ...
    for c in range(len(matriz)):
        for i in range(0, len(matriz[0])):  # alterei esta linha
            print(matriz[c][i], end=' ')
        print(' ')

Why Good programming practices in general ask us to do everything within functions-your code that creates a new array and that calls the array generation is out of functions and cannot be executed in such a way as to isolate the array, which is a global variable.

If you do this, it will work:

from random import randint

def gerar_matriz ():
    matriz = [[], [], []]

    for c in range(len(matriz)):
        for i in range(0, 3):

            s = randint(0, 9)
            matriz[c].append(s)    # adiciona os números a matriz
    return matriz

    def imprime():

        for c in range(3):

            matriz = gerar_matriz()

            for c in range(len(matriz)):
                for i in range(0, 3):
                    print(matriz[c][i], end=' ')
                print(' ')
        print ('\n')

    imprime()

All I did there was stop relying on The "Matrix" as a global variable - it is created inside the generar_matrix function and returned to whoever called the function. (turning the print code into a function is not essential, but prevents the "array" name from being re-named associated globally, and that other functions would see only the last Matrix generated).

Another thing is that in Python you rarely, rarely even have to use for with range. In general, we are interested in the elements of a sequence, not in the indices of the elements, and then look for the elements.

In the case of the array, we can do a for to get each row, and inside a for to get each element:

def imprime():

    for c in range(3):  # aqui sim, queremos repetir algo 3 vezes!
        matriz = gerar_matriz()

        for linha in matriz:
            for elemento in linha:
                print(elemento, end=' ')
            print()
    print ('\n')