Yes, please use Test.assertDeepEquals to compare objects and arrays.

expect(your_func(array1, array2)).to.deep.equal(array2)

The problem is if you compare [1] === [1] it will result as false. So you have to tell the test suite to compare individual elements of the array, not array itself. Becasue var a = [1] and var b = [1] are two different arrays (they have different reference to the memory).

Same issue, what would cause that issue in the test code?

Check your Test code.
Perhaps problem there

I go on to specify you may recieve input which is not a string and to handle that correctly.

The description also starts off by telling us to implement a function "which takes a string as input." Probably a good idea to reword this.

I have the same issue (but for what it's worth when I clicked submit my solution was accepted).

In the description it says you are only expecting strings if you receive anything different return 0 vowels and 0 constants :)