The var $! refers to the C library errno global variable. It is set in many places in the runtime system. errno is not explicitly reset by any library function.

You should only check $! if you know there is an error. (Such as after a failed open.) In fact, perlvar specifically states that it is meaningless if an error has not occurred.

In this case, you probably want $? which contains the error generated by the backticks operator.