Here's my rewrite:

#!/usr/bin/perl -w

use strict;
use warnings;
use Sort::Key qw(usort);
use List::MoreUtils qw(uniq);

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";
my @bug_array  = map {
    split /\s*,\s*/, $_
} $bug_fix_msg =~ m/\bbugs?\s*:?\s*(\d+(?:\s*,\s*\d+)*)\b/ig;

my @sorted = usort uniq @bug_array;

print "\n  sorted: @sorted\n";

print "OK!\n" if "@sorted" eq "3 17 24 42 50 58 99 456 1722";
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I started with your same test, and ended by ensuring that the sorted output matched what you had before. So, it at least passes this test. Just some quick notes... I drastically changed your regex. Instead of matching multiple commas between numbers, I now only match digits-(spaces?-one_comma-spaces?-digits)*. So, "123, 456" is good, "123,,456" is discarded.

Then I split each of the regex matches, and the split is that space-comma-space section. This gets rid of the spaces at the same time as doing the split, which makes it a bit less work to read/understand/execute.

Then the unique/sorting steps, I went to modules. List::MoreUtils is one of my favourite modules for useful tidbits of code where I don't have to worry about bugs. It's often faster than a hand-written version due to being XS, but it's always faster in developer time, once you're familiar with them. I don't have to think about it - I just call "uniq LIST". And then, rather than doing $a vs $b comparisons, I know that Sort::Key, which is also mostly native XS code, already does this. This shouldn't be much different than your version, but can be a tiny bit more explicit. Sort::Key has many other options for sorting, too, so you may want to get familiar with it anyway.

Hope that helps.

Update: Thank you for a) posting your code, b) describing what you wanted to do, and c) providing a built-in test that others could use to get a better idea of what you're talking about. Oh, and d) providing a negative test ("bug33r"). All VERY helpful. I wish I could give a ++ for each of these points.