It mostly happens when the streamed game has some sort of interaction with audience, can recall a few times it happened:
1.
Animal Crossing stream, someone visited his island to exchange goods or whatever, and then left a tranny flag on the bulletin. Joel then cut this part out in youtube upload.
2.
Mario 64 vs Twitch Chat, a few occurences of a message being sent into the game, including trying to trick him into pronouncing it (don't remember timestamp). Joel didn't buy into it.
3.
Meme House Charity Special, a random sim was spotted wearing a shirt in tranny flag colors added by EA. Joel could be seen zooming out the camera to get the sim out of picture, and one of the latter episodes shows this sim converted into Cultist Member, presumably after Joel asked Kirillian to do so.