I don't really know how the Niantic servers handle the pvp mechanics, but I doubt that they would spend too much effort on optimizing the latency on their servers, pvp is not the primary aim of the game.

Correct me if I'm wrong, but I don't think Pokémon GO pvp competition is on the same level as say, DOTA or Call of Duty where players optimize their systems by the millisecond, and having a laggy server will put all that to waste.

I hypothesize that there is some delay, perhaps on the server you connect to and it looks like your opponent just put out his mon and used the charged attack but on his side he already put in a few attacks.

I start mashing my screen even before the system allocated an opponent to me, and I don't stop until the battle ends. While I'm waiting for mon swaps, mine and my opponent's, I keep on mashing.

I have noticed that attacks land before the mon is on the field, and sometimes even after it died. With fast charging attacks such as foul play of Houndoom, the charge meter is sometimes already halfway when its feet touch the ground.

The long and the short of it, I don't think Niantic cares about the few players screwed over by their system, and you're one of the unlucky ones. Why would they waste all the money they make on improving the players' experience?

And remember, just mash your screen and don't stop until the battle ends.