There is an issue with homework but yours sounds a bit different
I have exactly the same problem. I don't use Mods and I haven't got any teenagers yet. It doesn't matter if she is doing homework on her own or getting help, just before she is finished it's like someone has typed in re-set sim. It registers that the homework is done, but it doesn't register on her aspiration of doing homework while focused. It's annoying because the homework stays on the ground and all the actions queued up for after the homework cancel. I agree... it is extremely annoying!
This sounds like the common issue: http://answers.ea.com/t5/The-Sims-4-Bug-Reports/When-kids-finish-homework-ALL-sims-stop-actions/td-p/5015388/jump-to/first-unread-message
It should only happen on beds, sofas and on the floor though. Try make them use a table.
