6 people stabbed Jon Snow but only 4 people got hanged for it. Jon Snow must have forgotten about the other 2 traitor's. Not to mention the other men who stood and watched him die.

Wasn't there a battle in the first 1 or 2 episodes? Presumably the other mutineers died then. Or perhaps they escaped.

This isn't a plot hole so much as something that's not spoonfed to us. Wikipedia says a plot hole is "a gap or inconsistency in a storyline that goes against the flow of logic established by the story's plot." Not every such gap of information is a plot hole; sometimes we just don't see every detail of the world.

The men from the Brotherhood Without Banners killed the villagers for no apparent reason and were subsequently killed off just as carelessly. This all served to reintroduce the Hound but it was a poor attempt. And the Brotherhood are supposed to be good!

As others have said, those were (to borrow a Fallout 3 NPC name) Brotherhood outcasts. That's why the BotB hanged them. This is explicitly stated in the show. Members of the Brotherhood went astray and the Brotherhood proper executed them for it.

Even with the benefit of hindsight, Arya's plot in Braavos lacks clear direction.

While this was true, I think the episode makes it clear that the Waif has failed her test.

Tyrion was wasted.

I agree. This has been the case since Season 5. It's sad, honestly -- Peter Dinklage has gone from the show's #1 star to a side character. I don't think that transition is required by the narrative, either. Tyrion, Jon, and Dany have always been the Big 3 (with Arya and Bran close behind).

The Frey's, the Tully's, and the Brotherhood Without Banners, who were previously forgotten, were clumsily rushed back into the story to either kill them off or set them up for the show's end-game.

I don't know why bringing them back for the endgame is a problem. My only complaint is that the Blackfish got such a shitty offscreen death.

Yes, there were plenty of dumb moments involving Sansa, Arya, Euron and the Dorne storyline, and they've been discussed already.

For the record, the way they included Euron was worse than anything else you've mentioned except Dorne.

And honestly, I don't think Dorne's conclusion would get the same hate had last season not been such a waste of the characters.