When Edward Douglas is rescued from the life-raft the shadows in the life-raft seem to indicate a different time than would be indicated by the position of the sun behind the rescuing boat. In fact if, as is implied, he can see the rescuing boat, the sun is in two completely different positions in the sky.
When first arriving at the gate to the compound in the jeep (12 minutes into the movie) a windmill is shown turning. As they enter, the view from inside the jeep shows it turning about half the speed, and the next shot goes back to full speed.
After witnessing the birth (24 min into the movie), Aissa guides Douglas to the beach. As they run through the forest, the light coming through the trees casts long shadows for the characters, yet as they emerge onto the beach they have no shadows at all.
When Dr. Moreau prepares to inject a drug into one of the "humanimals", the needle of the syringe is visible. After that visual switches away then back to Dr. Moreau, the needle is no longer there. It reappears right after while Dr. Moreau is injecting the creature.
After witnessing the birth of the humanimal baby, Aissa guides Douglas to the beach while it is obviously night time. After leaving the beach and running through the forest, they come out to a waterfall where there is bright sunshine and blue skies.