Plot hole: Any strike on a military facility by incoming aircraft would first take out the SAM sites with missiles to clear the way for said aircraft to operate freely. After all, the Tomahawks fly right past the attacking planes and take out the runway with no issues at all - no reason they couldn't hit the high and exposed SAMs.
Plot hole: Sam sent a post card from the church where the keys are used. But Sam was captured moments after locating the book that gives the clue about the church, and would never have had a chance to go there.
Plot hole: Vulture was able to re-create his suit despite the tech for it being confiscated when he was arrested. Also, the tech does not exist in the Venomverse, so he would have had no means of accessing it by any stretch of the imagination.
Plot hole: Zeus reassures the vast audience of deities in Omnipotent City that the God Butcherer won't reach Eternity, an omnipotent being that will grant one wish to the first person ever to reach it. This knowledge is fairly trivial amongst deities. This introduces the obvious absurdity that nobody ever tried to make use of this power to undo Thanos' damage. Also, Zeus just happens to know the bad guy's plan out of the blue.
Plot hole: During the shootout with Penguin and his gang at the warehouse Batman gets shot and falls to the ground. Penguin then creeps over to the spot he fell and realises he has disappeared and is in his car behind him. It is totally impossible for Batman to just disappear and get behind them without being seen, no matter the rain or firefight, that place was lighted enough and everybody was looking that way. (01:18:00 - 01:19:15)
Plot hole: Police Commissioner Clarke told arrestee Savage he could do 10 years hard time for armed robbery or "go inside Degnan [Correctional Institute] and get me what I want [evidence of civil rights violations]." Savage had not even been officially charged with any crime (s). A police commissioner does not determine what an arrestee will be convicted of or how much time will be served upon conviction. The Civil Rights Division of the Department of Justice investigates civil rights violations. (00:06:53)
Plot hole: Detective Knight's law enforcement jurisdiction lies within L.A. county (with limited exceptions, such as "hot pursuit"). It is absurd that he would be given permission, transportation, time away from L.A. duties, funds, etc. to go to New York - outside of his geographical jurisdiction - to continue an "investigation" based on a hunch about the robbers' identities.
Plot hole: At the end of the film, we see Nick Fowler is now in the job originally held by Larry Marks before he was killed. We know Larry was corrupt and that he admitted in front of numerous agents that he had identified Nick's body. Surely, there is no way the CIA would allow Nick back, let alone in a leadership role, without questioning why Larry would lie about Nick being dead. That alone would raise serious suspicions about them both, but we're expected to believe he walked right back in?
Plot hole: When Cage and his wife and mates are going to the FBI safehouse the FBI agent shoots 2 baddies two separate times whilst Cage etc. are ascending the stairs, yet they don't hear the gunshots.
Suggested correction: The idea was to use the tomahawks to take out the airfield and prevent enemy planes from taking off. The SAMs could be evaded by flying through the canyon so the airfield was considered a higher priority target.
lionhead
While that may be so, those planes exit would have a difficult time out running and avoiding that many SAMs. It's not like the ship wouldn't have enough tomahawks to take out the SAMs as well.
Taking out the airfield was deemed necessary to complete the mission, taking out SAMs beyond the canyon was not. The original plan didn't take into account the pilots surviving the mission in the first place, so the Navy didn't bother with extra strikes on SAM sites. Maverick had to struggle to get them to approve this plan in the first place too, so he wouldn't be able to convince them to put even more effort into it.
lionhead
They still have to avoid the SAMs on the way out, no canyon to protect them then.