Several comments:

Don't modify the array that you are for()'ing over. (Modifying the elements is fine, but inserting or deleting can have interesting interaction.)

Your code inserts # at the beginning of the array, not just before the "a", but once you find an "a", you move the a forward so you will find it on the next iteration of the loop, and then you do it again, and again... Try:

my @a = qw/x y z
a b c
e f g
h i j/;

my $skip;
for (@a) {
   if ($_ eq "a" && ($skip = !$skip)) {
      splice @a, 0, 0, "#";
   }
}
[download]

If you really want the "#" just before the "a", something like this is a lot easier:

@a = map {$_ eq "a" ? ("#","a") : $_} @a;
[download]