A few things I found:
The three girls in this Italian cartoon keep shrinking themselves smaller and smaller to spy on this guy. They're basically microscopic by the end and fly a helicopter right by his face as he's about to eat cake. I was kinda hoping they got eaten with the cake, but they get sucked up his nose and subsequently sneezed out:
https://www.youtube.com/watch?v=jqpPxF59frMThen there's two episodes of this anime. The first has these kids shrunk down and eaten by a cop, they take a trip through his digestive system:
https://www.youtube.com/watch?v=c7oUs0xcG6gAnd this one they're in the same cop exploring pretty much everything else I think:
https://www.youtube.com/watch?v=aPpL8vV-rYg^There might be more endo episodes/scenes in this series, but skimming the playlist I didn't find anything.
This small series of short cartoons has a pair of animals making their way through a scientists' digestive system:
https://www.youtube.com/watch?v=w1aCoMJllM0Last but not least, there's this anime in which a boy is eaten by a giant and goes through his digestive system:
https://www.youtube.com/watch?v=_KUJHCVxS7M