When your code removes a 0, another element of the array will slide into that slot---but your code will move on to the next slot and will not check that element. So if there are 2 0s in a row, it will check and remove the first 0 and ignore the second 0 because that now is at a position where the first 0 was already removed.

BTW: This is exactly the same kind of problem a for loop will run into if you change the array it is running over. So remember the old rule to never change an array you're iterating over unless you know exactly what you are doing.

Your algo is not that far of, just put the $i++ in an else block. (Or use a more perlish way, see the othe reply.)