Plot hole: When Sam and Dean realise they need to destroy the hook to stop the Hook Man, they find out that it has been reforged into something else. They state it needs to be set on fire to stop him, but if it was melted down and reforged then it has already been set on fire and the Hook Man shouldn't be latched on to it in the first place.
Plot hole: Marie says at the beginning that Chuck quit writing after Swan Song (season 5). Later she says she hates the "Metastories" which don't happen until season 9. She couldn't have known about the Metastories since those books were not published.
Plot hole: In episodes where Sam and Dean are required to perform spells/rituals at certain times, the issue not quite seen is that not all clocks are exactly in sync with each other, meaning that the clock they are using could be off by a few minutes especially if dealing with different time zones or time periods. (S07E12, Time After Time).