Really, I don't know how your data looks like or how you are getting it..
However, does something like this work for you:

use strict;
use warnings;

while(<DATA>){
 chomp;
   print $_,$/ if /\d{2}$/;
}

__DATA__
PHY/99/3006
PHY/99/3009
PHY/99/2678
PHY/99/390O
PHY/99/129R
PHY/99/UY90
[download]

PHY/99/3006
PHY/99/3009
PHY/99/2678
PHY/99/UY90
[download]

...I want to match the last 2 characters of any string (if numeric) that doesn't look like this:...

And here is your "this" explained that you don't want the last two characters to match:

/^[s][0|6]00[0-9]{2}/

    ^ Start of string

    Char class [s] matches one of the following chars: s

    Char class [0|6] matches one of the following chars: 0|6

    00 Literal `00`

    Char class [0-9] 2 times matches one of the following chars: 0-9
[download]

Your regex matches (or doesn't match) much more than the last two characters of any string. 2teez already mentioned your data, and it would be helpful if you would show a sample along with what you'd like to exclude from it via a regex.

use Modern::Perl;

while (<DATA>) {
    chomp;
    next if /^[s][0|6]00[0-9]{2}/;
    next unless /(\d{2})$/;
    say "$_ -> $1";
}

__DATA__
s00023
s50012
s600ad
s00012
abc-def-123456
[download]

The second test rejects all data that does not end in two digits.

If the data "survives" both tests it gets printed.

s50012 -> 12
abc-def-123456 -> 56
[download]