Some of our aircraft operate with double crew, the aircraft has a bedroom and toilet behind the cockpit door. Crews regurally change out of their uniforms during their rest period, they are also assigned passenger seats, so it would be very common to see someone dressed like a passenger enter the cockpit once descent had begun and they had woken up. Likewise for other aircraft types, it can be crew returning from the crew bunk. On smaller aircraft it could be the observer pilot, or even a crew member just getting back to base, or even the pilots wife!
So dont stress it!
Mutt