1. Stellar evolution:
I've noticed that the sun does not turn into a red giant when aged enough, and also it doesn't leave a white dwarf after its nova. No star actually leaves anything but gas and particle effects.
Also, it seems the hydrogen contents of main sequence stars remains constant over the entire lifetime, it's not gradually used up.
2. Degenerate matter bodies:
I think that when using the material system (or by adding matter by collisions), white dwarfs should turn slowly into neutron stars, and then, neutron stars turn slowly into black holes. Some exotic kind of deg. matter body could be added too (like quark stars between neutron stars and black holes)
And also, I've noticed that black holes do not grow when fed with the material system.
3. Black hole evolution:
Black holes could also have Hawking radiation modeled, so if one of them is light enough (so the background radiation does not actually make it grow), it evaporates over time.