print does not execute statements, arguments are first resolved like with any function. Your code is equivalent to:

>>> def pola(arr):
...     for i, item in enumerate(arr):
...             arr[i] = item*item
... 
>>> a = [1,2,3,4]
>>> pola(a)
>>> print(a, None, a)
[1, 4, 9, 16] None [1, 4, 9, 16]

I would close this as not a bug.