Both aren't bugs

1. The function was removed because the object should check for collision itself in either beginStep, step, or endStep IMO. Why? Because it will make collision resolving (what actually should be done if something does collide) much easier. I'm not saying that the .collide function is bad, I'm saying that calling it directly in the main loop was bad. As a cause of this the collision detection of bullets was temporarily disabled, causing you to think destroyInstance was never set.
2. The second is sort more of a known
issue. The current physics are just an example implementation by me until it gets replaced with real tested code.