Plot hole: In the course of the story it's said that at the time the black hole went out of control, it had a mass of "half a mountaintop of granite." But in a flashback scene Dr. Krone is shown growing the mass of the hole by feeding it large numbers of lead bricks in the laboratory. It's a little hard to believe his lab could store, or even afford, enough lead bricks to equal that much mass.
Plot hole: Tyler jumps into the water, then grabs his mask and puts it on and begins swimming, but he fails to clear his mask by blowing the water out of it. Without clearing it, he wouldn't have been able to see a thing.
Plot hole: Travis does the last time jump to change the events of a previous time jump. As all the jumps were to the exact same time to kill the same dinosaur, the travelers of the second jump must have found there the travelers of the first one. The travelers of the third jump must have found the travelers of the second and the first, and so on.
Plot hole: In the scene where The Commander and Jetstream are called to fight the giant robot, Will's mom says "What if he forgets his lunch?" In every scene where he's eating lunch at school, Will has a school lunch.
Plot hole: After E.D.I. goes rouge, Kara brings up his weapons list, which consists of 2 ThroatRippers, 2 ShockHammers, and 3 Blue Ferrets, so E.D.I. has 7 missiles. He fires two during the Russian dogfight, another two when he and Ben escape from Alaska, and another two at the Korean border - one of which is the last missile. That's 6. So where did the last missile go?
Plot hole: Even if Chicken Little was tagged out when he hit home plate, the game was already tied so his team would still have a chance to win the pennant.