"Confronting" is a strong way to approach a problem the 1st time.I'd suggest to him that perhaps his "friend" isn't really such a good buddy since he decided to help himself to stuff without asking/checking to see if it was okay.In a shared housing/community fridge that's a no,no.
I'd suggest you sticker your food/drink and perhaps put a note on the fridge reminding people to check and ask before taking anything if they aren't sure whom it belongs to.
As to the flushing issue,perhaps he was in a hurry,gave the bowl a quick flush and it just didn't go all the way down,don't say anything unless you notice that it's a reptative issue.