The bit I don't like is the "we".
How and why would it be "we"? How would it be a joint activity? To me that could mean two things
a) He knows exactly how it got in there and the "we" is an attempt to align himself with your genuine innocence.
b) He doesn't know how it got in there (prank) or has a good idea if it is a prank but doesn't want to say that as it looks dodgy/cover up, and the "we" is an attempt to mention it whilst showing without saying that he isn't accusing you of anything as "we" are equally in the dark about it.
Does he have any jokey/prankey mates or colleagues?
Has he shown any signs of anything to cause you suspicion?
More importantly, who is the one most "in charge" in your relationship? If he usually is, it's a bit suspicious that he would be so genial about something that to most people would look dodgy. Is it more likely he'd usually be serious about a serious matter?
If it's you, then it would fit in more that he doesn't want to upset you by pointing the finger and knows it's likely a prank.
The outside chance is that as other MN have said, it's a pre-emptive strike and interesting that they said that before you revealed you went in there for a missing lipstick recently.
Ultimately you did not put it there. That rules out you and leaves him and outside chance, a pranked.