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This isn't a bug and should be closed. It's more of a stack overflow question.
If you'd like to change this fundamental behavior of a very common operation in python you should make a proposal to the python ideas mailing list at http://mail.python.org/mailman/listinfo/python-ideas
In your example board_2 is equivalent to:
 row = [0] * N
 board_2 = row * N
All the rows are the same initial row. As opposed to board_1 where each row is a new row.
Try this:
 [id(i) for i in board_2]
The initial equivalence is because they do represent the same values (NxN list of all zeroes). What should python compare if not by values?