Hand 1 KK
For sure you should have raised this up preflop, and as played I would also have bet out on the flop. I dont think, KK is quite good enough to go for a check-raise, and I dont want it to get checked through and give everyone a free chance to draw out on me. Turn and river were standard value bets, and I also dont think, you can fold to his mini-raise. Sure you are normally beat, but you only need to be good 1 in 6 times, and god knows, what some players might show up with here in a micro tournament or a freeroll. Some cant even read boards and might think, 65 is still a great hand to raise for value.
Hand 2 AK
Raising and limping from SB is both fine depending on your overall strategy and reads.
Hand 3 AQ
I would also have gotten it in here. I dont think, undersized 3-bets are ALWAYS aces or kings. Sometimes they are, but more often they are just random goofing around from someone, who is not very good. BTN vs. SB ranges should be wide, so I think, AQ is easily good enough to go with it. If you just call, you miss the flop 2 out of 3 times, and then he will
bluff you out of the pot with his KJ or whatever. I would much rather force him to show me a hand, that beat my AQ, which unfortunately this time he had.
Conclusion
I think, you are being to hard on yourself. Apart from not raising KK pre, I dont think, you did anything wrong at all. And even if you did raise KK pre, he would not have folded, so you would still have lost and probably a much bigger pot. So mostly this was just run bad, and I would also have busted from these two hands.