Jealousy

Why would he tell his wife that her employee’s makeup looks good? Am I missing something?

Don't be so cocky. You can't be absolutely sure your boss's husband wants to fuck you.

Only 99% sure.

Hope your boss is into threesomes.

Yes you are! Bitches be crazy.

I’m confused, has he seen you with makeup on during your dates?

I’m confused. Please explain someone.

My thinking is that boss's husband has seen said coworker outside of work (while she was wearing make up) which sparked the comment to boss. Now the boss thinks that husband may be cheating with said coworker. Now if that suspicion is true or not, only OP can tell us for sure.

Given OP followed up with "he obviously never told his wife she looks good with make-up on," I'll wager he was trying to hint to his wife "see, That's how you do it" (after mistaking OP for having make-up on) or otherwise call his wife ugly.