Arrays in Java are zero-based, which means they start at index zero, and range until index array.length-1.
Your code starts the row and column at 1—which means you’re skipping the initialization of row/column 0. That’s probably where at least some of the problems are coming from, since you’re using your 5×5 array (rows/columns 0,1,2,3,4) as a 4×4 array (rows/columns 1,2,3,4).
There’s also the fact that your Encrypt method doesn’t actually make any assignments to the array. You probably want to initialize it like this:
// NOTE: changed return type to void -- this is a side-effect-only method!
public void Encrypt(char Encrypt[][])
{
// NOTE: use single-quotes for chars. double-quotes are for strings.
char aChar="A";
// NOTE: changed the starting loop values from `1` to `0`
for (int row = 0; row < Encrypt.length; row++)
{
// NOTE: technically Encrypt.length works here since it's a square
// 2D array, but you should really loop until Encrypt[row].length
for (int column = 0; column < Encrypt[row].length; column++)
{
// NOTE: set each entry to the desired char value
Encrypt[row][column] = aChar;
}
}
}
There are several issues with your original code. Look at the NOTE entries in the comments for individual explanations.