The two wire might also be tied in with the light to power a second light like the wall light over the vanity. Yes normally the 3 wire would be in the first light but if a remodel happened or the sparky just did it different it could be that way.
Another scenario is that the three wire may be the line in with a switch loop back although to switch both individually would have required improper use of the grounding conductor (which is common in DIY installations).
An electrician would be able to figure this out in a couple of minutes as Hotline suggested. Trial and error wiring methods are risky at best.
Last edited by BigB; 08/25/16 11:57 AM.