Plot hole: When the Drakes (Bobby's family) arrive home they are acting quite naturally, until they find Wolverine there and get a start. Later on we see that they had parked their van in the driveway right behind Cyclops' car, which Logan and company had borrowed and parked there. Wouldn't they, seeing a strange car in their driveway, be suspicious or at least enter their house asking "Bobby, are you home?" (00:52:45 - 00:59:15)
Plot hole: When Magneto lands the bridge between San Francisco and Alcatraz, only the ends of the bridge are on land, with the rest still suspended in the air despite having nothing to keep it there. Magneto could arguably be using his powers to keep it supported, but at the moment he loses his powers it still does not collapse at the center.
Plot hole: There are two timelines in the X-Men franchise - the original films and the prequels, up until Days of Future past, which alters the future, and at the end reveals that Jean Grey, Professor X and Cyclops are all alive, rather than dying as they did in X-Men 3. The "new" timeline is then followed in Apocalypse and this movie, giving them a bit of leeway to make changes, much like the new Star Trek movies. Only problem is...Jean Grey dies in this movie! So no way her older self can be around in DoFP.
Suggested correction: I think you might have missed the final shot in the movie, when the camera pans up from Charles and Erik playing chess and the Phoenix firebird is shown flying across the sky/stratosphere, implying that, much like the Phoenix's legendary namesake, Jean had risen from the ashes so to speak. There is precedent for this in the comics, plus there were supposed to be more X-Men movies after this one until the Disney/Fox merger happened.
Yes, but she even said she evolved beyond earth, so that is basically saying that she died. Or she isn't on earth anymore.
Suggested correction: Bryan Singer confirmed that the end of Days of Future Past with Jean Grey being alive is one of many timelines, there are more than 2 timelines in this universe, meaning that despite all the X-Men being alive in the future at the of Days of Future Past, they can still all die in other movies like in Logan and Dark Phoenix.