The past few times I logged out, when I logged back in, two pokemon that were in my roster (not box, but team), went back to my box. What is going on here?

That's an easy fix.
Go to 'Your Pokemon' and where it says:

Here you can manage your pokemon and set up your team.

If you want to send slots 2-6 to your box click here.

Click 'here', and then redo your team. Log out and back in again, and that should fix it.

[you must login to view links]
read