Plot hole: In Series 1, Episode 7, "The Dumpling Paradox, " Sheldon makes an oblique reference to his financial status: "Frankly, if I could afford the rent, I'd ask you [Leonard] to leave, " meaning he cannot pay the rent on his two bedroom apartment by himself - not that he doesn't want to, he can't. However, in "The Execlsior Acquisition, " we find that he does not even cash his pay cheques. He doesn't even deposit them into a bank account - he leaves them in a drawer in his desk. In Series 2 Episode 14 "The Financial Permeability", he lends Penny a large amount of money from a huge bankroll he just happens to have lying about - again, without cashing his pay cheques! He is obviously independently wealthy. Either he doesn't have enough money to afford the rent or he has enough to work without being paid while practically giving large amounts of cash away. Can't be both.
Plot hole: Near the end, Sam locks Mr. Howard and Ms. Briggs in a closet. Sam and Gibby then put a heavy desk right against the door and leave them stuck inside. Then later the two teachers are seen frantically controlling the students. How did they escape? They were inside a closet with the door locked on the outside and with a heavy desk against it.
Plot hole: When Linda (Mom) gets home from her cooking class and greets the boys, she sees nothing out of place. However, just a few moments before, we see the giant laser in the corner of the yard that they forgot to attach to the laser-inator. Wouldn't she have seen this?
Plot hole: Casey needs to get Devon's hospital keycard in order to get into the secure holding area to plant the listening device into the pacemaker before it's implanted into the terrorist. They obtain the key-card by stunning him at his bachelor party and see Casey using it to access the storage facility, backed up by Chuck and Agent Forrest. We then see the terrorists scanning their leader and detecting the implanted bug - Devon is listed as the surgeon. Immediately after this, we cut to Devon waking up from his bachelor party with his keycard missing. None of the three agents involved in planting the bug could possibly have handled the operation, no other agents are mentioned as being present and, as the break-in occurred during the daytime, the staff of the busy hospital would have noticed had an unknown surgical team suddenly taking over one of their operating theatres. So Devon apparently got into the hospital with no key and did the operation while completely unconscious.
Plot hole: (Ep. 5) The weapon Stephen finds in a desert is a H&K G36. He states that it's not a military weapon and is mainly a mercenary weapon. The G36 is used by several police and special forces units in the world, including the British SAS, which could suggest another nation's or British government branch's involvement. Comment was probably made to deepen the intrigue of the season plot.
Plot hole: When Maria Jackson is running away from the alien creature, she turns left into a metal fencing. The camera shows this seconds before she runs into it, banging on it in frustration. This does not make any sense. She saw the metal fencing, so why did she continue to run into it? Why did she not turn right instead and along the park?
Plot hole: In Part 1 look closely when Cassie is showing Maddie the 'Oblivion' website that contain pictures of her. Some of the pictures are those we actually see being taken of her in Part 2 (the following episode). How could they be on the website before they've even been taken?
Plot hole: When Justin and Juliet were trapped behind the glass and Juliet let herself be captured by the mummy, so she doesn't burn to ashes when the morning comes, why didn't Juliet just escape? The mummy gave her enough time to turn around and share a moment with Justin, she could've used that time to fight him off, break Justin out and escape. The mummy wasn't very strong and Alex would've shown up 20 seconds later anyway, there wasn't any real reason for Juliet to just let herself be taken away.
Plot hole: I believe in the very first episode, during the flashback when Mick remembers rescuing Beth and killing Coraline, we see him stab her with a wooden stake, which is supposed to paralyze a vampire, as said in the "Dr. Feel Good" episode. However when Mick looks back with Beth in his arms, Coraline suddenly gets up and watches him leave while burning to "death." This is simply not possible; in the "Dr. Feel Good" episode, Mick could not release the stake himself and asked Beth to do it. This also happened in the episode when Josef was staked by the hit man that was hired to kill him, (in the episode where we meet the woman, Sarah I believe, that he accidentally put into a coma after attempting to turn her). Again, Josef was unable to remove the stake himself and Mick had to do it for him, so there is absolutely no way Coraline would be watching Mick and Beth leave; she would still be on the ground possibly burning to death.