None of your moves were really terrible, but on many of them I was thinking "eh, that doesn't feel right."
Umm, I guess the overall consequence was you became passive. You were happy to sit back and defend even though you had the worse pawn structure and your c1 bishop was inactive. I was looking for chances to develop the bishop or play f3 or c4. Trading your only good minor piece (16.Be2) felt especially incorrect.
I stopped looking after black blundered the knight, but in the position before that happened, for example, your d2 bishop is embarrassing I mean, it's almost better to just give away a pawn than get stuck with a piece like that.
There are a lot of things I like about the move 20.a4, but first piece activity, pawn moves come later.
As for your specific questions, sure, Nf3, Ne5 and defending mate with the bishop... those were all reasonable. I don't think those moves are the main theme of your inaccuracies / mistakes.
When I reviewed this game I realized I'm making defensive moves based purely on what I see with no real guiding principles' on what is typically best. Be interested on peoples thoughts on what they would play as the defensive move in each situation and why. Comment 13 & 18 in the diagram with my thoughts!