Plot hole: The "video history" of the crashed USAF ship makes it very clear that the planet is uninhabited when they "landed". I can understand how a race of apes develops - they had a bunch of them on board. I can understand how a race of humans develops - they are descendants of the original crew. What I don't understand is...where the heck did all the horses come from?
Plot hole: At the very end, when Leo Davidson crash-lands in Washington, DC, on the very steps of the Lincoln Memorial, the modified Lincoln statue depicts General Thade (the founder of the ape civilization on Earth) as wearing mid-19th Century clothing. This suggests that Thade escaped from his home planet Ashlar (aboard the recovered single-passenger Delta Pod, no doubt), entered the time-rift, and arrived on Earth in the early-to-mid 19th Century to begin taking over the human population. So, Thade by himself (with no advanced scientific knowledge) completely conquered human civilization on Earth in only about 150 years, which is absurd even for space fantasy.
Plot hole: We know that Pericles the chimp (in Alpha Pod), then Leo Davidson (in Delta Pod), and then the entire Oberon space station are all pulled into the time rift and end up on planet Ashlar, each arriving at (drastically) different times. Apparently, just before the Oberon crashed on Ashlar, Commander Vasich sent a mayday transmission ("We're going down!") which is actually received by the Oberon itself before it entered the time rift. Commander Vasich and the Oberon crew are startled to see a very elderly Commander Vasich in the mayday transmission. This implies that Vasich and the Oberon crew instantly aged by decades while going through the time rift; yet, Leo Davidson and Pericles the chimp didn't age at all.