I suppose you don’t remember the last thing you did before stuff stopped working? The mines seem to be the common link so maybe mining is messed up. But yeah what you are experiencing is basically something that happens when an animation doesn’t finish properly and the player gets locked into a state of thinking you are performing an action. Since it thinks you are doing something all the time it doesn’t allow you to act. It used to be far more relevant but from what I understand the bug obviously still exists but is somewhat rare.
So, for the tree thing can you actually walk through the tree trunk? As in the object literally doesn’t stop you, or does the tree just appear in front of the player when you are close? I ask because those are two very different things, one of which is a far larger problem than the other.