Plot hole: When Vlad enters Mehmed's tent, the entire floor is covered in silver coins and Mehmed remarks on Vlad's weakness to it. There's no way that Mehmed could have known about Vlad being a vampire or about his weakness to silver, as Vlad had killed every Turk after becoming a vampire, so nobody would be alive to tell him. Even the Turk found on the battlefield in the morning lived long enough only to deliver Vlad's message, but died immediately after that.
Plot hole: SPOILER: When Amy comes back, doctors would have checked her non-existent head wound from the "abduction", from where she supposedly lost that much blood. That would and should have revealed all of Amy's lies.
Plot hole: There is no logical reason to switch off the Bombe at midnight when the codes change. Firstly, Turing's proving the concept of automated code breaking, so even if it only finds the right settings days or weeks later, the experiment is worth doing, then you can work out how to speed it up to be operationally useful. Secondly, even in steady state operation, cracking "yesterday's" settings (and thus intercepted signals) is still going to be pretty useful in most cases. Threatening to smash the Bombe up at midnight is good stuff to add some movie tension but, in reality, it's nonsense.
Plot hole: After Hannigan feels guilty for what she did, she confesses to the girls, and they find Mr. Stacks to tell him. The fact is, they went straight to where he worked - but Annie never told them the destination, and Guy himself never told Hannigan where it was either. So, how did they get there, and most importantly, know where it was?
Plot hole: Lamar was a star basketball player who didn't pay attention in Jim's English Literature class (and wasn't "good in English") but needed to pass to continue playing. Lamar told Jim, "I've had four courses with you" and "I'm a Junior." Whether this was Lamar's 4th or 5th English course, neither make sense. A fourth course would equal 12 credits - enough to be Lamar's' declared major (unlikely) - and most students don't enroll in the same professor's courses when they don't do well ("easy A"). (00:43:56 - 00:46:40)
Suggested correction: It's not a plot hole, it's how they operated it in reality.
I have a copy of British Intelligence in the Second World War, by F H Hensley (the official historian and ex-GCCS). I quote page 309 as an example - 'the knowledge of the Tracking Rooms was far from perfect on account of delays in breaking the settings...During the first half of 1943, however, while the traffic was read with delays that were sometimes less than 24 hours, days when the settings proven to be unusual stubborn were not uncommon...Between 10 March Andy the end of June the setting standards for an a further 22 days were either not broken at all or broken only after a long delay.'...'A delay of as much a said three days in learning that U-boats had been ordered to move to new position so could thus mean than intelligence was received too late to be of use in diverting convoys'. So pretty clear that they carried on attempting to crack the settings well after the end of a day so they can process intercepts which might still be relevant.