Strangely, Police DenLiner's headquarters on DenLiner seems much wider than train itself, especially when compared to other rooms such as the dining car.
How Negataros and the other Imagin in this movie survived Kai's death and the destruction of the Imagins future time in the Den-O finale is not explained. Owner describes Negataros as a 'stray'.
Although Negataros stole the spare Rider Pass from Owner, it is unclear where he got the Nega Den-O belt and Nega DenGasher.
Sieg says that Liner Form is the form of Ryoutarou fighting alone. However, he forgets to mention Plat Form, which Ryoutarou also uses without an Imagin partner.
Sieg tells Hana that he possessed Ryoutarou in 2000 because they came to see him in the past. However, as he was dropped off in 1997, he could visit them at any time as he would still be living in their present, 2007.
Owner says that God's Line allows travel back tens of thousands of years, something which other time trains such as DenLiner and ZeroLiner cannot do. However, when Yuuto was collecting Ryoutarous for the Climax Scene, ZeroLiner travelled all the way back to the dinosaur era, at least 65 million years in the past.
It is not revealed how Gaoh came into possession of the Kamen Rider Gaoh belt. Given that it shares his name, he may have built it himself.
It is unclear why Momotaros didn't just use the Den-O belt himself to activate Sword Form instead of possessing Kotarou as the other Taro Imagin have done.
As Momotaros and Urataros fight in the ally, the overhead shot shows Momotaros kicking over a burning bucket, but the shot of Ryutaros and Naomi immediately following this shows the bucket back in it's original upright position.
Although KingLiner was briefly seen dropping Ryoutarou and Yuuto off in 2007, it was neither seen before, after or mentioned and played no further part in events.
Somehow, the Kai in 2007 knew that the Albinoleo Imagin would be emerging from his body at that specific time and helped to open the time portal. Previously Kai and all other Imagin contractors have not done this (as the Imagin emerges into a time from before they formed the contract in the first place).
Ryutaros' possession of Ryoutaros during the battle against the Armadillo Imagin somehow activates Den-O's change into Gun Form without swiping the Rider Pass over the Terminal Buckle as everyone else did during that fight.
Kai's diary says that December 12th 2006 was a Sunday when in fact it was a Tuesday.
Strangely, the two boys who remember Yuuto don't seem to notice ZeroLiner parked a few feet away.
For some reason, possession by the Oct Imagin causes Shoko's bracelet to glow.
In the jump cut between Shoko entering and exiting the clothes shop, all the t-shirts on the rail outside change positions.
The cut scenes from this episode show Deneb cooking in the previously unseen ZeroLiner galley.
Owner must have grown several feet for his run alongside DenLiner for his head to be level with the dining car's windows.
In the cut scenes, Deneb collapses onto Machine ZeroHorn's right turn signal.
Somehow, as DenLiner and ZeroLiner went underground, dirt got into the ZeroLiner cockpit although there are no windows or other open areas in that part of the train.