There is more than that though! Paige and Henry get left, often at no notice and in weird ways/places. They get left alone in the middle of the night. (This is one I think Paige is specifically aware of as maybe being Weird - that's why she was checking the bedroom door, seeing if they were in the house.) They have some really bizarrely strict house rules. They've had at least one time where Elizabeth is clearly really worried/panicked, but doesn't explain why and instead is all "we're going to a movie! ...oh wait, I need to leave you at a movie!" The Jennings don't just lack a family, but they lack any friends at all on top of that. (Unless you count the Beemans, and they're new.)

Any single one of those could easily have any number of explanations. It's the combo of all of them that equals Something Is Up. :)

And I really hope Philip didn't denounce his dad (but it's definitely possible). I don't think Paige is going to get as far as denouncing, though. At least not until the very end of the show, and that would be such a sad way to end!