Perhaps your algorithm is wrong or perhaps your data isn't what you think it is. Here is an SSCCE:

#!/usr/bin/env perl 
use strict;
use warnings;

my @a2 = qw/foo bar baz/;
my $match = join '|', @a2;
my @a1 = qw/bar quux/;
print grep {$_ !~ $match} @a1;
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This prints one blank line (for "bar") and one line with "quux" in it. Do you understand why?

Amended thanks to AnomalousMonk for pointing out the error.