Jamie's swimming lesson aside, the final battle did have a couple of moments that made me go "why the hell did they do that?". These are not "plot holes", just things that don't make a whole lot of sense.
The first was Dany taking out the Lannister soldiers by flying across the line. This created a gap for the Dothraki to pour through, so fair enough. They also set a record by having 20 stunt men lit up for the stunt, which is apparently a world record. Question - why would she not fly along the length of the line, toasting the entire army? From a military perspective, this makes little sense. The answer is probably cost - 20 stunt men was a world record, lighting up 200 stunt men probably would have blown the episode's budget completely.
The second was the decision to toast the supply wagons. We watched her fly repeatedly along the supply column, roasting one wagon after another. Why? She has an army stuck in Casterly Rock, with no food... and here she is destroying a column full of supplies that the Unsullied desperately need. Why? Probably because it looks pretty on the screen, even if it makes very little logical sense. Presumably this battle takes place not far from Kings Landing (given that the gold makes it safely to the city) - it's a long way from Casterly Rock, so who knows if the supplies would have even made it there in time. Could well be a moot point, so I'm not overly annoyed by it. It did make for very pretty pyrotechnics.
Looking to more positive things... I loved the sword battle between Arya and Brienne. Outstanding. I also liked the scene with Bran getting the best of Littlefinger. I figured "chaos ladder" was significant somehow, but it wasn't until I read this thread that I made the connection with Littlefinger's season 3 speech. Kudos to those who picked this up so quickly.
As for the poisoned crossbow bolts... I'm not sure. The idea hadn't even occurred to me. The biggest impediment would be a lack of knowledge regarding Dragon biology, given that they're magical creatures. I certainly wouldn't put it past Qyburn to coat the barbs with a concoction of the deadliest poisons he could come up with, and hope for the best. It will be interesting to see how this one pans out.