It's known that the cruise ship and any surroundings after leaving it is in a time loop.
Though Jess remembers the ship and tells Greg, she makes no indication that she is in the time loop. So yes, the movie was meant to confuse the user but seeing that, according to the number of dead Sallys on board, the time loop occurs more than 20 times.
So the first time she entered the loop, the storm sent her into an alternate reality with the neverending timeloop? Is this what the movie was showing? I noticed there is a deadly Jess that was not really in the foreground that got shot in the head, and stabs Sally and Downey in one of the rooms. I cannot really place where she falls into the picture seeing that one of the previous Jess instances killed that Jess instead of letting her jump overboard.
So is there a separate timeline/reality?