Factual error: It is not possible that Pitt could have gone up to the ship when it was already blasting off. There was literally fire in the tunnel.
Suggested correction: It was a bit confusing, but what I saw was a shower of sparks or hot particles and some fumes, and no fire in the tunnel until he was through the hatch. The makers may have been influenced by seeing vapour prior to a rocket launch, and then some rockets use a shower of electric sparks to ignite the engines. It was implausible, but no fire in the tunnel.
Other mistake: One visual that has always bothered me that I could not find in your list were the scenes when the mother ship first appears. It's enormous scale appears to dwarf Devil's Tower and the whole surrounding area actually, but when it moves over to the "landing strip" area and begins to rotate 180° (right-side up?), it suddenly seems to shrink to a much smaller size and mass during the slow revolution. On its originally-seen scale above/behind the tower, one would think that either the great ship's outer prongs would have been torn off, or more likely the impromptu landing site and most of Devil's Tower would have been destroyed as the huge craft rotated itself. The visual scales just do not stay consistent throughout the film's climactic final act.
Continuity mistake: When the WABAC machine is going through the time vortex, trying to escape from the black hole, some tiles get sucked off the WABAC, but in the next shot they are back on.
Visible crew/equipment: After Indy and Henry have escaped from Castle Brunwald, Indy jumps into one of the boats, pulls the motor starter cord and jumps back out, then just as he bends over to release the boat from the piling, right between Indy's legs the black covered arm of a hidden crewmember appears from under the tarp taking hold of the throttle, steering the boat away from the pier. (01:02:40)
Factual error: Denham is obviously shooting a sound film - he has a sound recordist with him along with the bulky and awkward recording equipment typical for the era, and they discuss the problems of recording dialogue on board. But not once do we see him filming with sound. We see the crew recording dialogue - synchronised sound, recorded on location, which is utterly impossible given the equipment they have and the circumstances under which the fim is being shot. We never see a microphone, a boom pole or a tape recorder. His camera isn't even 'blimped' - soundproofed - and it's handcranked, which makes a racket. They can't be planning on adding the sound later - why have the sound recordist and his bulky and heavy equipment there with them if they are? We see the crew recording dialogue - synchronised sound, recorded on location, which is utterly impossible given the equipment they have and the circumstances under which the fim is being shot. The whole point of post dubbing dialogue is that you don't need a sound recordist in the first place.
Factual error: It is roughly 120-135 dB inside of a C-130, especially one that hasn't been specifically modified. It is so loud that it is painful to be in the cargo hold without hearing protection (besides it being outside of military regulations) and you certainly couldn't have a normal conversation while it was in flight.
Continuity mistake: On the ship, Dr. Zimsky reveals that project DESTINI is an acronym and that the last letter is "I" and not "Y." (INI standing for INItiative). When Rat is at his computer, he goes to the website for Project Destiny, with a "Y" and not an "I." This same thing happens when the Project Destiny subtitle flashes across the screen.
Factual error: In the movie, we see the Statue of Liberty with its current bluish-green color. The statue only got that color over time, and as it was still being built, it should be its original brown.
Factual error: Mel and Goldie board a ferry. A visible sign states 'Detroit-Racine Ferry'. Detroit is on the east side of the state of Michigan but Racine, Wisconsin is west of Michigan, across Lake Michigan. The only water route to get from Detroit to Racine would be to circumnavigate the entire state of Michigan.
Visible crew/equipment: During the Quidditch match Harry's broomstick tries to shake him off, due to the spell. After Hermione tells Ron, "Leave it to me," in Harry's last close-up before he flips over, the seat that is attached to the broomstick, to make it more comfortable for Dan Radcliffe to sit on, is entirely visible. Glimpses of other seats can be had during the match as well. (01:20:50)
Continuity mistake: When Karl Urban is defending the Asgardians, the dust covers on his rifles vary between being open and closed several times. M16 dust covers are sprung loaded - they open on the first shot and have to be manually closed afterwards.
Continuity mistake: When Xenophilius draws the Deathly Hallows symbol, he draws it so that the bottom of the line touches the bottom of the circle. The shot cuts away and back again when he draws the triangle, but the line is no longer touching the bottom of the circle. (01:49:40)
Other mistake: Even though it is snowing throughout much of the movie, none of the snow seems to stick to any of the characters' fur. Even during the fight scene when they are rolling around in it, they are never covered with white.
Continuity mistake: In the beginning scenes, where Milo Thatch is practising his proposal, he slides over (face forward, chest against the board) a chalk drawing of a map detailing the location of Atlantis. When he realises he wiped off the drawing, and sees it on his clothes, he stands in front of the blank part of the chalkboard, "filling in" the space with the map that rubbed off on his shirt - the only problem is, that the image should have rubbed off backwards as he was facing the board when it transferred to his clothes. He could not simply stand in the place of the missing map face forward and have it read properly.
Revealing mistake: When the UFO makes the huge flash that knocks everyone in the cemetery down, one of the police officers kicks a tombstone as he falls and it wobbles back and forth. (00:13:35)
Factual error: When the barracks are completely flooded, Eggsy uses his bare fist to punch through a large two-way mirror to escape. The fact is that any glass (or plexiglas) thick enough to contain hundreds (or thousands) of tons of water without bursting would be as impenetrable as concrete to Eggsy's bare fist. He would need a chisel-tipped jackhammer to penetrate such a mirror.
Plot hole: There are six metal bars mounted around the circumference of the water wheel's axle. In the wheel's interior, when Jack frees himself he lands on his feet, begins to run and promptly hits his head on one of those mounted axle bars, then falls out. Moments later, when Jack returns and runs in the wheel, he is shorter (way more than a foot) than all six of the mounted axle bars spinning with the water wheel, which would make that previous shot impossible, however humorous it is. (01:52:40 - 01:53:55)
Continuity mistake: When Magneto lands the Golden Gate Bridge on the island, as it hits land it is still very light. When the Brotherhood start to walk toward the island, it cuts to a wide shot of them still walking on the bridge, and it's suddenly dark.
Continuity mistake: At the beginning of the movie, Harry's van has bucket seats, yet later on when the "gas-man" rides along, he is sitting on a bench seat in-between Harry and Lloyd. (00:38:00)
Suggested correction: Mental isn't sitting on a bench seat, it's implied he's sitting on the floor of the van in between the both of them. Although hard to see, the backs of the bucket seats can still be seen behind Harry and Lloyd at certain points. You see a fair bit of it behind Harry whilst he's dancing as Lloyd sings the line "and if that mocking bird don't sing".
Factual error: That is not a crocodile that attacks Sue. It more closely resembles an American alligator - the squat, rounded snout gives it away. Australian crocodiles have a much sharper, more angular snout. There are other tell-tale physical features, most notably the placement of the alligator's teeth when it closes its mouth, but that's the main one.
Suggested correction: You can tell by the shape of the snout and the ridges above the eyes that, although animatronic, it is meant to be a Marine Crocodile that is native to Australia. It doesn't resemble an American alligator, which doesn't possess those pronounced ridges. Also, freshwater crocodiles can be seen in the boat ride scene where Mick motions for Sue to lean up off the edge of the boat. They have the narrower, angular snout that you referenced.
The placement of the alligator's teeth when it closes its mouth shows that it is more like an alligator than a crocodile. In fact, the animatronic puppet is a bizarre mish-mash of physical characteristics of both crocodiles and alligators.