It works fine for me:

use strict;
use warnings;

my $s = 'a foo about foo above foo across foo after foo afterwards';
$s =~ s/\ba\b|\babout\b|\babove\b|\bacross\b|\bafter\b|\bafterwards\b/
+/g;

print "$s\n";
__END__
 foo  foo  foo  foo  foo
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BTW, you can tighten that regexp without loss of generality:

$s =~ s/\b(?:a|about|above|across|after|afterwards)\b//g;
[download]