Around 1:20, the two motorcycles go from driving on the outside of the train track rails to the inside, then at 1:21, one is inside and one is outside.
When Isaac is taking the lie detector test he is asked where he was on Wednesday and Thursday of the previous week, and he answers that he doesn't know. Earlier in the movie he told his coworker that he went hiking on Saturday, and his coworker told him it was Wednesday, so he did know where he was on Wednesday having been at home the night before his coworker asked him.
At about 37 mins, the waitress pours Isaac's coffee from an orange-topped decaf pot, but he didn't order decaf.
At 4.54 the sign above the JPL door is labeled as Jet Propultion Laboratory. It should be Propulsion.
When Carl tell his abduction story, he says that it was Thursday, November 7, 1979, but that date actually fell on a Wednesday.
At about 36 mins, when the salt and pepper shakers float through the air near Isaac, the contents of the shakers are not affected by gravity.
At 20 minutes in, there is a dart board on a brick wall. A dart player would not mount it there without proper backing to protect the darts and the periphery..
1.06.45
Camera crew reflection to the left.
The distance from Costa Rica to British Columbia, as the crow flies (not up the coast as they traveled) is 3800 miles. The Cessna Seaplane they fly in has a range of 482 miles and cruises at 140mph. It would have taken 27hours and they would have had to refuel 8 times. Going the coastal route would have taken much longer and more refuels.
Aliens removing the tracker from Cyprus' arm took much much more time than they took in removing the tracker from Sara's arm, while Carl and Sara were shot dead outside. Though the entire special effect was for show off, efforts should have been made to keep the timings almost same to make it more believable.
Going by even the most liberal definition of Abduction, Cyprus was not at all abducted. He was not touched, he was not captured, he was not taken anywhere else. He just witness a series of events and shot it, but it doesn't make him getting abducted. So this aspect was an outright lie on the video he had released, and it adds to people not believing his version.