Even though the main explanation is consistent and ties the whole movie together there are still a few parts of the movie that are not explained and have to rely on theory. Here are some of those questions with possible explanations and some common mistakes people make.
Why exactly does a Tangent Universe (TU) occur? Are they a natural phenomenon or are they artificially created. There is one theory that scientists in the future build a machine that somehow causes a rip in time back in the past. Another theory is it could have been caused by Alien involvement.
Quite a common thought is Frank saving Donnie in the beginning is the cause of the TU. Donnie was meant to die and by surviving he altered things which caused the corruption. This is not true though, we are already within the TU when Frank wakes Donnie up. Frank's special powers only work within the TU so he would only be able to wake Donnie after the TU had started.
The same goes for the Artifact not being the cause of the corruption. The jet engine appears several minutes after the TU had started. The Philosophy of Time Travel states that the Artifact is the first sign of evidence that a TU has occurred.
One major question is where does the jet engine in the beginning of the movie come from originally? If it came from the future where exactly and what day did it come from?
A common answer to this question is it's the same engine Donnie sends through the portal from the plane his mother and sister were on. The engine travels through time and lands on Donnie's house. It's exactly the same event as the end of the film only the first time round Donnie survives.
This is extremely unlikely though as the portals are just a gateway between the two Universes. The first engine lands in the Tangent Universe (TU) so if it came through a portal it would have to come from the Primary Universe (PU). The engine Donnie rips of the plane at the end is from the TU and travels through a portal into the PU so there is no way it can be the same event repeating.
If it did come from a future point in the PU once the corruption is fixed by Donnie that future event won't happen now so we will never find out exactly how it occurred.
Another theory is the Tangent Universe is a copy of the Primary Universe but as it's being formed there is a glitch or copying error. This error produces a duplicate engine that is then dumped into Donnie's bedroom. This anomaly makes the TU even more unstable and it must be sent into the PU.
Roberta Sparrow writes the book "The Philosophy Of Time Travel" which helps guide Donnie but how exactly did she know all this information? There are a few plausible explanations for this. It seems like she had a similar experience herself so either she was a Living Receiver or one of the Manipulated Dead in a previous Tangent Universe.
Both options would in theory give her all the information required. If she was a Living Receiver she would obviously have known what to do and the Manipulated Dead have a large understanding of what is happening within a Tangent Universe. It's possible she may have somehow retained some of the information from her experience once the Primary Universe started up again.
This subject is one of the most debated parts of the movie. A lot of people make the mistake of thinking Donnie waking up and cheating death in the beginning is what caused the Tangent Universe (TU) to occur. The assumption is then once the Primary Universe is restored Donnie stays in bed otherwise he risks causing another TU to start and the whole cycle will repeat. This theory is not correct though, Donnie and Frank have nothing to do with the creation of the TU.
We hear about other Living Receivers in The Philosophy of Time Travel who were killed by the Artifact they returned. If we include Donnie then it seems the Living Receiver always dies once the Primary Universe is restored. The question is what would happen if Donnie got out of bed again and survived? The moment we see Donnie laughing in bed at the end the Primary Universe is already restored. If Donnie got out of bed and dodged the second engine after that then in theory nothing would change as the corruption is already fixed.
Another important point is whether Donnie chooses to die. The Donnie we see in bed at the end is not the same Donnie from the last 28 days. How much knowledge he has of what happened in the TU is very questionable and it’s quite unlikely he knows he is about to die.
The question of destiny plays quite a big part here, Donnie was meant to die but Frank saved him. It’s possible he was chosen as the Living Receiver because his life is now expendable; he is going to die anyway. Once back in the real world it's Donnie's destiny to die.