Straying off an assigned path to go to an uncharted planet while being responsable for 2000 colonist.
Not really a plot hole, just bad writing if you want to see it that way. But... Oram is actually quite eloquent and logical about why they should deviate from their course and check it out. After all, the planet seems perfectly inhabitable and poses no major deviation within the 7 year time span in hypersleep
Tech more advanced than prequels.
So it was in Prometheus... And they actually did a decent job of mixing high tech with some older looking stuff. As high tech as the Covenent is, it's no where near as top of the line as the Prometheus
Not sending probes before landing.
Neither did the Nostromo, the Sulaco or the Prometheus. All these ships and crews seem to rely on the ship's advanced sensors
No environmental suites on an unknown planet.
Yeah, maybe they should have worn environmental suits... 
But seriously, the ship's sensors had already mapped out the entire atmosphere, they even mention it in the movie. They wore environmental suits in Alien and Prometheus because the atmosphere was toxic
Containment protocol not followed at all.
I'm kinda lost here... when? Faris quarantined both Ledward and Karine, and later when Tennessee brings them all back into the Covenant, there's no reason to believe they're infected, as infection affects the host almost immediately, and none show any symptoms
Scientists not caring about the 1st encounter with a civilized alien race city.
They just had disastrous and traumatic losses, were clearly in danger and needed to be evacuated as quickly as possible. Were they really supposed to care about a dead alien city in that moment? Stop and look in wonder? Take notes? 
Only 1 city on the entire planet.
Do we know that? And if there were only one, why should there be more? Because we humans cover our planet in them? Aren't these guys supposed to be more advanced? Seems you're being very homocentric about the whole deal... if humans do it, then every other intelligent race has to do the same...
Even on earth, aircraft without permission are shot down and yet David was able to bomb a more advanced race with their own tech.
Again, you're judging the engineers as if they should act like humans. Besides, the craft that arrived was one of theirs. How are we to know what their entry protocols are?
How did David have any test subjects to be able to perfect his creation. Everything was dead.
No. The black goo only acted upon human and human-like DNA as far as we know(like that of the engineers). And even if the black goo had an effect on every living creature, still David could keep experimenting with the black goo on different species until he perfected the "extremely violent" creature whose sole purpose was to destroy all biological life
Who layed the eggs? It seemed like David lived in a cave.
One of David's experiments with different species he mutated with the black goo. Or maybe he morphed subjects into them. At any rate, it's quite clear the eggs (and the resulting facehuggers and xenomorphs) are David's crowning achievement up to that point
Why would the xeno attach a machine/ crane when there was living pray right in front of it.
I thought it was defending itself and then trying to get back into to ship
Acid splatter misses everyone.
Well, bullets also miss a lot of people... didn't bother me really. Seems to me it's just one of those things people like to complain when they want to find fault
Facehugger acid melted through layers of the ship in alien, but barely injured someone in Covenant.
It also took a hell of a lot of time to melt through Hicks' face and armor, didn't it? But, again, this is a first iteration of these things, they are not the facehuggers and xenomorphs from Alien
Facehugger can now implant an embryo in 10 seconds.
See above
Walter could self heal but Ash, Bishop, Call, nor David could.
They were all different models. Must be pretty expensive tech, the one used in David. Walter even mentions that he is a more evolved model. Also, Walter did not suffer such catastrophic damage as say, Bishop or Ash. Also, remember that even Walter could not grow his hand back. So the self-healing is only for smaller wounds
Etc.
in any case, it was a good way to wrap up the Alien and Ripley's story. 
