Dead Freight - S5-E5
Plot hole: Preparing to steal methylamine from the train, Walt, Jesse and Mike measure off a predetermined distance from the railroad crossing, which happens to coincide with a handy arroyo, where they bury their tanks. Problem is that they couldn't have known that distance (calculated by knowing the position of the methylamine tanker car in the train) until Lydia told them. But she didn't call that info in until the night after they'd already buried the tanks.
Suggested correction: They were counting on the tankers being at the back of the train, far enough away and at a curved angle so that the conductors wouldn't see them, and the hoses they were using would have been long enough to reach the tankers on either side of the one they stole from. Their heist hinged on a lot of educated guesses and luck, especially because they would have had to abort if the tanker was at the front of the train, but being lucky doesn't make it a plot hole.
I'd have to respectfully disagree. When they paced off the distance to the trestle over the arroyo, they had a particular number in mind (814). It's not explained whether this number represented knowledge of how far back the tank car would be if the engine stopped at the crossing. But if it did, how could they have known that? Not even Lydia knew until much later. And why would they assume the tank car would be toward the back of the train? Lydia doesn't mention that. When she calls Walt, all she says is, "I've got it." And even if she were to tell him, at that point everything's in place for the heist to happen at the location where the tank are buried.
IIRC the crew contacted an expert on hazardous materials shipping for advice on the scene. Rail guidelines require tankers containing hazardous materials are at a minimum "six-deep", that is, six cars away from the engine. Lydia probably told them in advance how long the train would be in terms of cars, so they had a rough guideline for which three or four tankers could possibly contain the methylamine. From there, it seems like their hoses were long enough to get to any of the other cars.
The 814 feet was to ensure that the spot they chose would be far enough away from the conductors so as to not be seen. And they weren't assuming the tankers would be at the back, they were just hoping they would be. As I mentioned, if the tankers were at the front, they wouldn't have been able to move forward with the mission. Lydia told them they would only have 6 hours to prepare for the heist after she told them where the tanker would be. That wouldn't have been enough time for them to get an excavator out there and dig the holes for their own tanks to transfer the methylamine into, so they had to guess the best spot to do it ahead of time and hope that's where it would end up being.
Strawberries and Cream: Part 1 - S3-E23
Plot hole: In the heat of killing fake Red John, Jane forgot to notice that Craig O'Laughlin never knew about the mall setup to lure Red John. So definitely Gale Bertram himself was in contact with the serial killer which he may have missed first up, but all that time in jail afterwards he could have figured it out.
Plot hole: Parker gains access to the external room using a valid security card, they figure out the CEO's passcode which opens the burn room door...and yet the room inside is still protected by a swarm of lasers. Was the CEO supposed to dance through the laser sensors like Parker does every time he goes in?
Plot hole: When the guys break into the safe house and free the witness against Bobby, they are wearing masks to hide their identities. Yet after freeing the witness, Jax and Tig decide to get involved in a fist fight inside the house which would leave their DNA all over the place. Since both are undoubtedly on the police database, it would take no time at all for the police to find at least two of the culprits who assaulted two officers, an ATF agent and intimidated their star witness.
Plot hole: At the very end of series two, there was a shootout during an armed robbery. WPC Granger somehow had access to a firearm. Surely the fact of her uniform rank would not have allowed this.
Triumvirate of Terror! - S3-E8
Plot hole: After Superman thwarts Lex's plan and knocks the Kryptonite into the sewers, Lex yells in frustration, splits his power suit off and flies away on a jet pack. Superman just lets him go. Wouldn't Superman chase him and catch him, especially seeing as how weak Lex would be like that? (00:07:35)