We are given an explanation of the time travel experience that says the time traveler’s body sleeps as his mind takes over a past version of his body–something like astral projection but that it is temporal and the spirit must be in a body. That introduces our next problem.
It is perhaps the most hectic moment in the film, as Xavier’s team bursts into Trask’s private meeting just as Mystique has been discovered by the Sentinel tracking system. They prevent her from killing Trask, but then Magneto attempts to kill Mystique to prevent Trask from ever being able to obtain her DNA (messy solution that, since her body would still be full of her DNA and it would be difficult to remove it from the premises without losing some along the way), and she escapes but is injured. Wolverine is in pursuit when he sees a familiar face, someone who is going to cause him a great deal of pain in the future, pain which he remembers vividly now and which disrupts his connection to his past body.
At the future end, Kitty is worried that she is losing the connection, and that Wolverine is awakening. This is odd. There is no indication that Kitty has any knowledge of what is happening in Wolverine’s history, and we were told that the changes would not be effected until he awoke; he has been in the past for probably over a day by now (and Kitty must be exhausted) since he has already run the Pentagon breakout and flown to Paris. There is no reason for Kitty not to allow him to awaken; of course, there is no indication that she has anything to do with that, but she does seem to be struggling to hold the connection at that point.
Meanwhile, at the past end, the past consciousness of Wolverine emerges. He does not remember Xavier or Beast, or understand how he got where he is. This disoriented state continues for what seems several minutes, long enough for Xavier to invent an explanation and move Wolverine to safety, and for Mystique to escape.
The question for us, though, is what happens to the time travel? Our understanding is that Logan’s mind is in the past because it is connected to Logan’s past body, but it seems at this moment to have become disconnected; is it returning to the future? Does it then return to the past? Is this still the same trip, or another?
If it is another trip, then by the logic put forward in the film once Logan leaves the past all of history should play through to the future. It is already a different future–Mystique did not kill Trask in Paris, although she was still seeking to kill him; Beast and Xavier were already working to prevent that; Magneto was also aware of the situation and acting in his own interest in this. We cannot reconstruct the future with any certainty, but the suggestion is that the Sentinel program is going to receive even more funding now that Mystique attempted to kill Trask, and still has Trask to make it work because she failed. Their situation in the future might be worse; they might not have had this chance at all. On the other hand, it might be that Wolverine’s actions have already been sufficient, that Xavier and Beast working together, possibly with others such as Quicksilver, might succeed in creating a better future; in that case, Wolverine would not return, because once he leaves the past Kitty will not be waiting to send him back again.
We thus must conclude that it is still the same trip, that despite the disruption Wolverine’s future mind is still in the past–it just is not controlling his past body. It might be bouncing forward a bit, picking up his body a minute or two later because he skipped to that point; it might still be in his past head, as it were, but temporarily overcome by his past mind. When he reconnects, it is still the same trip; the only disruption is that for a few minutes he was not in control of himself.