Plot Hole: When the military went to the other dimension and found Victor, he suddenly had a shawl on that he wasn't wearing when he was left behind originally. Where did it come from?
Plot Hole #2: When Victor escaped from the restraining bed, he wasn't wearing anything. However, Victor walks into the dimensional machine and comes back out wearing the shawl again. This makes no sense as earlier when he was brought to the facility he was wearing the shawl while being carried on the stretcher. This likely would mean the shawl was either confiscated or it was back the room he just escaped from and not on board the machine.
What Doesn't Make Sense: Toward the end of the movie, Victor kills Johnny and Sue's dad Franklin Storm. After the Fantastic Four defeat Victor, they seem to all but forget that their dad was just murdered. Johnny attempts to name the new headquarters after Franklin Storm, but Sue mentions that he wasn't one for wanting his name used that way. They then proceed to joke about what to name their newly formed team and then the movie ends. There is no funeral, no grieving or anything. It was odd that no one seemed to care about losing their father and mentor.