Hey thanks to everyone for your help. I decided to use jwkrahn's method, but I also realised that my regex wouldn't reject "bug,,8 bug,9". So I've added a lookahead to the regex filter. As follows: 
#!/usr/bin/perl
use warnings;
use strict;

my $bug_fix_msg =       "this 33,44 is a fix for mybug44,99 real \
                        bug 99 again   bug33r bug1722,3 bUg:99, \
                        bugs:456, 17,   24 bugs 42,58 bug:  50,50 \
                        buggy99 bug3,:8,34 bug,,49 bug,84 bug:s12";

print "test string: $bug_fix_msg\n\nFiltered:\n";

my %unique;
while ( $bug_fix_msg =~ /\bbugs?:?(?!,)([\s\d,]*)\b/ig ) {
    print "$1\n";
    $unique{ $_ }++ for $1 =~ /\d+/g;
    }

print ("End Filtered\n\n");

my @sorted = sort { $a <=> $b } keys %unique;
print "  unique:  @{[keys %unique]}\n";
print "  sorted:  @sorted\n";

[download]
Output as follows: 
test string: this 33,44 is a fix for mybug44,99 real
                        bug 99 again   bug33r bug1722,3 bUg:99,
                        bugs:456, 17,   24 bugs 42,58 bug:  50,50
                        buggy99 bug3,:8,34 bug,,49 bug,84 bug:s12

Filtered:
 99
1722,3
99,

456, 17,   24
 42,58
  50,50

3

End Filtered

  unique:  50 3 58 17 456 42 99 24 1722
  sorted:  3 17 24 42 50 58 99 456 1722

[download]
Thanks again for the help. I've always thought of regex parsing as a bit of a black art, but I'm starting to get the hang of it.

In reply to Re^2: Better way to do this, regex etc. by mintz
in thread Better way to do this, regex etc. by mintz

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