Anyway to hide quests that you skipped and they not available no more?

Let's say if there is 5 quests in the chain, and you did 1, 2, skipped 3, did 4 and 5, this 3rd quest still showing up as "Not Collected".

Agreed! I would like to know this as well. Just finished a bunch of Draenei quests on my Human Priest and the only quests left are a few Draenei-only ones and a few that I accidentally skipped by doing the rest of the quests. I also have my settings set that it would filter out any quests not for my race, but the Draenei ones are still there. I’ve restarted and I’ve refreshed. Nothing has helped with it. So between both of those issues, I’m not able to finish Azuremyst Isle.

This are the 2 quests, that cannot be completed anymore because i skipped them by doing next quests in the chain.

These quests are considered Breadcrumbs and are optional in terms of their completion. Unfortunately, there is currently no way for us to eliminate breadcrumbs from the listing if their follow-up quests have been completed. It is on the TODO list to resolve so it'll eventually get cleared up, but it currently isn't high on the priority list.

Some things that I have noticed people get confused on with quest tracking that I'll explain. It may or may not pertain to this particular issue as I'm not sure which quests area are affected. @badbranni @MrTylerKnight

If you have the option Show Incomplete Quests turned on this will show every single quest in ATT which is handy for things like Dailies, World Quests, rares, repeatable quests, etc.

If you are wanting to track quests done via a zone you want to have only Treat Quests as Collectible turned on. This will remove any quest that we have flagged as repeatable (and hopefully breadcrumb, but not sure at the moment).

If you have just Treat Quests as Collectible on and see quests that are repeatable, daily, world quest, optional, etc then if you can provide us with the specific quests name so we can verify and make sure it's marked in the database correctly.

If you have Show Incomplete Quests turned on then seeing them is an intended effect.

Following up on this issue.
As of commits 155f165 and 2aaddfe, quests that are flagged as breadcrumbs no longer count against you; however, do make note that Show Incomplete/Repeatable Quests must be enabled for you to see them in ATT.