Superficially, I'd kick this back in code review because the else is "cuddled" and you're not using a LABEL: with the next. You're also don't have use strict; use warnings;. More deeply, you don't need the if and the $Y{$y}++; looks to happen regardless.

Untested reduction, removed implicit $_ for clarity:

use strict;
use warnings;

my %Y = ();

MAINLOOP:
while (<>) {
  ...
  my ($y) = ... ;
  next MAINLOOP unless $y;
  $Y{$y}++;
INNERLOOP:
  foreach my $arg (@ARGV) {
    next INNERLOOP if $y eq $arg;
  }
}
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