Character mistake: While he may not have figured it out the moment he found the forest dying, certainly a botanist like Freeman Lowell would know plants need light to survive.
Revealing mistake: When McDonald is in the tunnels and is called to pick up the phone, he picks up a red phone. It is a standard Bell TouchTone desk phone. To make the phone look more futuristic, there was no cord and it was disguised as a cordless phone. The port that the cord would plug into is covered by a piece of colored tape. This also can be seen in the operations center of Ape Control when the worker picks up the phone.
Factual error: The colt .45 that Telly Savalas uses didn't come into use until 1911 (the film's set in 1909).
Continuity mistake: Pickett Smith has his shirt sleeves rolled up at the movie's beginning, then they're rolled down and buttoned then rolled back up before his canoe gets knocked over.
Revealing mistake: The protagonist jumps from a bridge and boards the train to try to save the Professor. When he is walking on the top of the carriages, look at the treetops in the background; the train is stationary. (00:12:00)