There are four problems that make the story confusing to understand on first view, and which may also pose problems for ever making Sense. Comments regarding the latter I will put in italics.
- nature of time travel
- timeflow of the story POV
- multiple simultaneous boxes
- revisiting the party
The central problem is the fundamental nature of time travel: "what happens if you change the past". The characters debate this, and say they don't know. For most of the movie, they simply don't resolve it. The only evidence is the cell phone message, where they "break symmetry" but with no ill effects. As best I can tell, Carruth expected us to infer from this sign the fundamental nature of time travel in this universe.
That nature appears to be that, when someone emerges after travelling back in time, they create a brand new "timeline" or "universe". In that universe, it doesn't matter what happened in the previous one; they can stop themselves from getting in the box without affecting their own existence, since their own existence is contingent upon the previous universe, not this one.
But this doesn't become clear for a long time. Eventually, the "failsafe" box is revealed; but the failsafe box doesn't "reset" time and let him try again; it lets Abe disrupt time and try again only by knocking out the "real" Abe and taking his place. The knocking-out of Abe is shot in extreme close-up where I couldn't even tell it was Abe; the narration presents all the information (about how long a person can be knocked out for and etc) in reverse order, so you're not clear why he wants the drugs and water etc. (e.g. you're thinking "hmm, how long could you stay inside a time machine?"). As a result, I didn't even understand the basic on-screen actions that were happening. (Actually, I'll revisit this a little more in point #2.)
So he goes back, knocks himself out, if you're as confused as I was you're not quite clear that that's what happened, and that the past can be changed, you're just absorbing that, and he goes to confront Aaron. Aaron repeats the same lines of dialog he did the first time--and this is supposed to be crazy clever because it's Aaron having previously recorded it and replaying the events, but the first time you encounter it, you (a) don't know he's done that, and (b) don't know the rules of the universe for sure--so it looks like HIS side of the world is playing out like it always had, and you can't change the universe, and Abe drops away stunned because of maybe that. Then immediately revealed is Aaron's headphones playing the previous events and you're just put in a total WTF and information overload.
Problem: Traditionally, we imagine this as a bifurcation process; the universe where the guy got in the box keeps going forward and living out its own thing, and meanwhile there's another universe. Which universe is shown in the story is a POV question. If that is supposed to be the case here, there are several problems, and then what's the deal with the Weeble. (This didn't involve strict time travel so maybe it gets a bye, but it technically was doing the same old back-travel, some 660 times... 660 bifurcations?) If it's not bifurcating--this seems to be implied by some of the narration--
Bah, this is taking too long to write up, so screw it. I think point 1 I'm pretty clear the issue why I think the movie is horribly confusing. Let's move on.
The story shows very few repeated events. The only thing repeated is the park bench scene. Supposedly the story follows Abe's POV (according to interviews), but that's clearly not the case when we don't get to see his first trip through the box. So let's ignore that claim and just think about it on its merits. Clearly, if the universe is bifurcating, we have to pick one branch to see past the bifurcation (we can watch multiple branches for a little while past it, but eventually the story has to pick one or the other). If it's resetting, though, then, essentially, once somebody goes into a box, everything past that just doesn't exist. Of course, in the new version of the timeline, somebody else can still enter a box that goes back even further...
So how does the weird granger plot make sense? In some other universe we never got to see, he ends up finding about the time machine and using one, for purposes we don't know. When he pops out of one of the boxes, we bifurcate/reset, and so whatever that future was, we'll never get to see it. But, we know everything leading up until the moment he pops out of the box have to be the same. We can presume everything after that is the same until he first causes their reactions to change. So, what we have to do is speculate that there was a previous timeline where he didn't disrupt them, they went and did there thing with stopping the car alarm guy, they never woke up and had that conversation, and then... something happened, and eventually Granger goes back in time. But...
Remember I'm not saying this is impossible or inconsistent, I'm saying why this story is confusing: all of the above happens before the failsafe is revealed, and thus before we even know what the nature of time travel in this univse is. In fact, here's where I added that comment to point 1 above about expanding on this down here, the whole plan Abe proposes ("we'll just scare the guy off and then never get woken up and we'll have never done this") doesn't fit the rule of the universe, which we don't even know anyway. Why does Abe think this will work? Has he experimented with causality and paradoxes in unshown scenes? It makes the scene utterly confusing because we don't know why it should work.
Why doesn't his plan fit the rule of the universe? Because, from what we know, if he actually did the plan, they wouldn't get woken up, wouldn't go back in time, and there'd be a pair of doubles! But he doesn't mention that this would be an issue! Yet, minutes later, after encountering Granger, he decides to use the failsafe, and knows he needs to drug his double, so he does know something about the nature of time travel here.
If you reset a timeline by emerging from a box, then the events from that timeline, after when you emerged, never happen. So how can Abe and Aaron get in two different boxes and still come out together? Abe emerging ought to reset the timeline, so it doesn't matter whether he gets in the box in this timeline, he'll have emerged regardless. This is especially problematic when they got out at different times! In a bifurcating universe, this just won't work; they'll each bifurcate separately, or something. In fact, maybe there it would work; there's a universe where Abe emerges first, doesn't interfere with Aaron getting in the box later that day, and thus that then spawns another universe, and in this one Aaron emerges. Under the reset model, I'm not sure how it would work at all.
Note that if this doesn't really work, it's not a plot point the movie needed to rely on--if there'd just been a single box big enough for both, you could have the exact same plot without this confusion.
Both plot timelines I've read try to have Aaron going in a box "simultaneous" with Abe going into his failsafe box, with them going to different times, and this is unworkable, but it's also not actually in the movie--presumably Abe goes back, and goes through events again with the same already-failsafed-Aaron, but who reacts to him differently this time since Abe is now fail-safed. Although I guess this is the basis for understanding why there are three Aarons, two of whom go away.
The party: this is really #1 again. The problem is, how do you constantly go revisit a party to try to get it right? (1) if you get shot you're screwed, you can't get in the box and try again; (2) when exactly did Aaron do this, and with what box (we want to assume that when Abe hears that Aaron was the hero, that's after Aaron has already iterated for the right outcome--but then when they're debating it, Aaron talks about three memories of the story shared between the two of them--why 3, if he iterated it tons of times); (3) what the hell is the narration talking about when it said he has to imagine he was just one iteration short? What the hell?
Heck, it's seemingly told in flashback even though apparently it's just as "now" from Abe's POV as everything else was.
My main complaint is that a lot of the above stuff is just unnecessarily confusing; it's fine to introduce a little confusion to reflect that of the characters, or to have twists and reveals, but these should be explained coherently, not leaving us grasping at straws to decipher them. My secondary complaint is that I have my doubts that you can form a single coherent storyline and time travel theory that resolves all of the above issues, rather than just some.