The problem is you're trying to iterate over an array that you're changing. You enter your loop and set $x to 1 (which occupies index 0). You then shift '1' out and lower the indices of all remaining elements. When you hit the beginning of the loop again, $x is set to 3 because it's now in index 1. You then shift 2 out and your loop exits because there's nothing at index 2 (or index 1 for that matter).

my @arr = ( 1, 2, 3 );

for my $x ( shift @arr ) {
  #do some stuff
}
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Edit: What the hell was I thinking when I wrote that? I meant to write the while loop that BrowserUk wrote below. Please do not use my answer. It doesn't work.