The first bite marks Gwangi leaves on the styracosaurus disappear in later shots.
When the spectators flee from the arena, one ticket booth is knocked over, leaving the open side facing up. In later shots a closed side faces up, and still later this same booth disappears completely.
When Lope's shirt is torn, the rip changes sides several times.
The pterodactyl picks Lope up by his shoulders, but when T.J. is cleaning his wounds there are several claw marks down his right side and none on his shoulders.
When the pterodactyl is in flight and shot from a distance its color is a bluish purple however,in the close ups it is either blue (if animated) or black, when full size, but not animated.
A line of dialogue points out that the Eohippus has three toes on the front foot and four on the back. This is the wrong way round - the animal had four on the front and three on the back. It is only the dialogue that is in error - Mr Harryhausen's model has the correct arrangement.
The curtain around Gwangi's cage is lifted with a huge gas balloon. The gases used in balloons did not become commonly available until decades after the film's setting, and remain very expensive; obtaining an adequate quantity of gas to fill this balloon in rural Mexico circa 1900 would not be feasible.
Lope tells Tuck Kirby that the arena is two miles outside of the town, which is confirmed when Tuck encounters Professor Bromley's paleontological digs in the open desert during his return from his first visit. Despite this, at the film's climax, the arena is clearly within the town. However, the later arena is clearly a different building with much larger grandstands. It is never stated nor implied that the climactic show is taking place at the same arena seen at the start of the film.
The little desert valley would not have enough vegetation to support one Styracosaurus let alone the amount that would be required to keep the species alive, which also means there wouldn't be enough meat to keep the Allosaurus and its brethren alive. However, the (painted) vista shown when the characters arrive in the valley shows that it is much larger than the small area where the action in the film takes place.
Gwangi's apparent color, as well as the color of the other creatures, changes several times over the course of the movie because there was so much animation to do that Harryhausen did not have enough time to do proper color testing. Gwangi ranges from gray to violet to purple from one scene to the next.
The circus elephant is still breathing even after being killed by Gwangi.
When Gwangi is chasing the cowboys out of the valley through the rock pass, one person falls off his horse twice.
The streets in the Mexican towns are paved with asphalt, which did not come into common use as a paving material until after the advent of the automobile. The streets would either be unpaved or paved with bricks or cobblestones.
The arena entrance is adorned with the 48-star United States flag, which was not introduced until 1912, about a decade after the film's setting.
T.J. and other women in the Wild West show wear hairstyles, makeup, short skirts and booties typical of the late 1960s, when the movie was filmed, and not the period of the story, 60 years earlier.
Modern utility poles are clearly visible in the town around the arena.
In the end chaos a number of people run into a church (pursued by the dinosaur). Some men outside try to open another set of very large church doors to let everyone back out to escape (or to assist in fighting the dinosaur once inside themselves). They are unable to open the doors, but keep trying to. In the utter chaos they surely cannot know how many people ran inside via another entrance, and the doors they are pulling are opaque. When the people trapped inside free themselves and emerge through the doors however (which were locked from the inside and that explains the difficulty the men outside had), the men outside see them come out, and immediately retire without looking inside and cease trying to help or get in, even though no words are exchanged. How did the men outside know the few people who emerged were the entire trapped contingent? For all they know there could still be people inside with the dinosaur.
After the group's encounters with the dinosaurs, there is no mention of nor do they seem concerned about finding El Diablo.
It is never explained or made clear how the gypsies knew where the show where Gwangi was being put on display was taking place. While it's not out of the question that the gypsies might have follow Tuck, T.J. and their group back to the town where the climatic show takes place after their encounter in the desert, there's no clear indication that they did and therefore, should not know where the show was taking place.
The creature Bromley refers to as a pterodactyl is actually a pteranodon. Pterodactyls did not have crests on their heads.