Tip #2 from the Basic debugging checklist: print. Add more prints inside your for loop. It is likely that $a is beyond the last element of the @matching_values array.

for($a=0;$a<=scalar(@hfr);$a++)
{
my @matching_indices=indexes {$hfr[$a]}@gl;
my @matching_values=@gl[@matching_indices];  
print "a=$a\n";
use Data::Dumper; print Dumper(\@matching_indices);
print "$matching_indices[$a]";
}
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