Well the main issue with different instances of an array is it can be confusing. For example, the way event picking works is if you pick more than one array instance it will be writing to two arrays at the same time. And this all happens "invisibly" - it's hard to check which arrays are being written to and what their content is.
It's clearer to think about if you only have one instance of an array. If you need multiple 2D arrays, use one 3D array instead, or different array objects if possible. On the other hand, if you know what you're getting in to, I guess you can go ahead and use multiple array instances!