Your problem is that the $_ in grep{/$_/} @pcov isn't what you think it is. You want it to be referring to your regex from @realassert, but as you have it written, it is an element of @pcov.

Also, the way you have it written results in empty elements in your final array (or undef if you remove the quotes from around $theline). Take a look at this approach:

#!/usr/bin/env perl
use strict;
use warnings;
use Data::Printer;

my @pcov = qw( junk yphs.pc0.samelogic.fois_ebs.sbetrgt_inst nothing )
+;
my @realassert = qw( stuff sbetrgt_inst other);
my @thelist;

foreach my $regex ( @realassert ) {
    push @thelist, grep{ /$regex/ } @pcov;
}                                           

p @thelist;
[download]