Ok, not plotholes, but these are nitpicks. They don't ruin the movie at all for me, but after having seen it for a third time, they stood out.
1. Batman can pretty much sneak in and out of most places undetected, yet triggers a break-in alarm at Wayne Enterprises? I'm talking about the scene before Fox sees the sonar system, when the secretary informs him that there was a break-in at Wayne electronics. I don't think Batman would do it intentionally, as if he wanted Lucius to come down there, he would have just told him to.
2. How does Joker get bombs into the hospital and ferries without being noticed at all? This took major planning on his part, at least a few days in advance, and I'm sure someone would have noticed someone moving that much explosives into those places.
3. How is Joker the only one not affected by the explosion at MCU when he was standing next to everyone else?
4. If Harvey had flipped the burnt side when he put the gun to his head, how would he have flipped the coin for Gordon?
5. How did Batman get to the top of that tall skyscraper in Hong Kong? He was in his batsuit, so unless he just walked in past security with a bag carrying the suit, without being questioned at all...
6. Why would Alfred ask "How do you say 'Apply your suntan lotion'"? Wouldn't he want to apply the lotion on the girls if they asked?
I dont remember the scene with Fox happening the way you just described.
I remember. You see the oxygen mask when he's first talking to Lucius, and again when Wayne is talking to Alfred about hiring a plane. But you don't see it at all when he's in Hong Kong.