- The disappearance of Ethan's father. Note that he never actually died in the accident. Instead, the changes automatically shift to the point of Ethan bringing him through the Hole into the present.
- The death of Irving's mother. Presumably, a Pen user can subvert their own immunity, but only by their own choice.
- Possibly, this immunity was extended to Kori. Over decades of being outside time, she eventually became immune to being simply 'erased'. The girl from the ending was actually Kori as Ethan knows her. While things were changed such that Kori Prime grew up normally, history asserted that there would have to be a Kori just like the one that was outside time, including all memories of Ethan. Because of the extent to which history asserts itself, this Kori would also be genetically identical to her 'mother', meaning there would be nothing incestuous about a relationship between her and her 'cousin' Ethan.
- Possible extension of the theory - stable time loops kick in whenever a user tries to pre-maturely erase another user, like the one we saw in the prologue.
- It's probably possible to kill another Hollow Pen user through manipulation of time, but the death cannot be directly caused by another Hollow Pen user. Irving's mother manipulated the bus so that it would crash, killing herself and her son. Even in these actions of suicide, the ripple effect will attract another Hollow Pen user in an attempt to prevent this scenario from happening.
- We know Ethan's pen was his father's before him, and that in the true timeline, he inherited it on his 17th birthday. Ethan sending the pen to himself in order to escape Irving's interference is a Stable Time Loop, but lacks a force-quit command. There's still a Hollow Pen out there that belongs to Ethan.
- Morris didn't drop out in the final timeline.
The Portal Gun and Hollow Pen are very similar to each other; they're both handheld devices for travelling space and time respectively using portal technology and it is established that ApSci worked on time travel.
- Combining the Hollow Pen and the Portal gun into one device... *shudder*
The green Pen only seems to work when it glows, which only happens when you have flashbacks, which in turn only happens when time has been altered by a Pen. Therefore, for the green Pen at least, previous digging is required in order to start your own digging session, in which case how did the first Hollow Pen user dig? I remember Ethan mentioning that more experienced Pen users like Irving have more and different types of flashbacks than he does, so it seems logical that the workings of the Pen changes with experience. Of course, that still doesn't solve the problem of the first Pen user, who would have not been able to use the Pen in this scenario due to a lack of time alteration prior. The only solution I can see to this problem is that the orange Pen has extra, unknown abilities that allows its user to open holes at will, unlike green, which can only alter changed timelines.
- Perhaps the pen changes colors as the user gains experience? The pen was green for Ethan and his dad because neither of them were experienced with it, but Irving's was orange because he's had decades of experience with his pen.
Well, he is bending time in all directions. Perhaps the Pens are the Keys to Time 2.0.
The fact that there are two Hollow Pens in a single small town seems unlikely, unless you take into consideration that Hollow Pen users are attracted to each other. So, while Irving and Ethan have been battling across the time line, other Hollow Pen users feel this vibration and lure them closer. That would be great Sequel Bait, that Pen users come in pairs, if not more.