I'm not very familiar with Sage's T5018 processing, but here are things that will make Sage leave employees out of T4 reports.  Maybe they will be similar enough to help you.

1. No SIN (or for T5018 BN).

2. Nothing entered on the first line of their mailing address.

3. No earnings this year (I know you've probably already checked this, but I wanted my list to be complete).