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.
Factual error: The "whaling boat" is too small to function as such. It isn't large enough to hold a fin, let alone disassemble a humpback whale.
Factual error: Teddy wears army boots that did not exist in 1959.
Factual error: The clan people look nothing like Neanderthals, they look like Cro-Magnon with a little dirt on.
Factual error: When Fievel is being dressed by the pigeon there are two American flags in the background. The flags have too many stars for the mid 1880s, when the movie is set.
Factual error: The aircraft are definitely post-WWI. Biggles is flying a De Havilland Tiger Moth, which appeared in 1930s. The German fighter is probably the PT-23 Stearman.
Factual error: In the scene outside the pub, a Ford Sierra is seen driving past. These were not introduced into the UK until Autumn 1982. The film is supposed to be set in 1981.
Factual error: Throughout the film, they play one of Strauss' Four Last Songs, which is credited as being "September." The song actually played is "Beim Schlafengehn."
Factual error: When the alien craft speeds away from the NASA base, its slipstream tears off the roof of a small booth. But the wake also should sweep the people in its flight path down to the ground; it is too close for that not to happen.
Factual error: Mission control begins an auto-landing sequence for the shuttle, but mission control did not have an ability to remote pilot the shuttle when the movie was made and wouldn't get it until 2006.
Factual error: Apparently, Ratigan had to cross the River Thames to reach Big Ben from Buckingham Palace as evidenced by him tossing Fidget into the river before taking reign of the blimp. However, the two landmarks are on the same side of the river.
Suggested correction: Ratigan changed direction multiple times during the chase because he was trying to get away from Basil. He may have flown away from that side of the river, but then after changing direction he flew across to the side he came from again.
Factual error: One scene shows the elephants bathing. During which you can see a car/van passing behind the trees in the background.
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.