IMO the most obvious case of things not working for continuity is Ohranger VS Carranger.Revival magic is a thing in sentai.
You've been told this before, the yokai in Kakuranger and Ninninger are born from completely different energies, one is more like a series of cryptoids while the other is born from magic shurikens interacting with objects.
Japan takes up a lot of square miles, there is nothing in GoGo-V that contradicts the events of Ohranger. On top of that GoGo-V also has one of the companies that appeared in Megaranger and one of its one off characters reappeared in Timeranger.
From the Ohrangers' point of view, the special takes place after their own series. IIRC they specifically state that they've already defeated Baranoia and the villain of the special is one final member that had escaped them until now. As has been mentioned, Ohranger begins in 1999 and the final story arc contains a one year time skip so it must be at least 2000 for them when the special occurs.
On the flip side, Carranger has a new year episode that specifically mentions that it's now 1997. On top of that, the combination of Carranger villains that appear in the special only appear in the show for about half a dozen or so episodes, which includes the new year episode. So it has to be either 1996 or 1997 for them when the special happens.
So yeah, the special has to be out of continuity for one of the two.
Lets just be honest, these shows are not made with an overall continuity in mind. That's before you add all the flip-flopping as to how it connects with the Kamen Riders.
Because starting the TV broadcast with the second episode would be confusing as hell for a lot of very little kids. It's really just a sneak preview to try and tempt more people into buying cinema tickets.And now Type Moon is influencing Sentai. Why not have it as episode 1?
Given the backstory mentioned so far, I'm guessing it will either show the Kikainoids escaping from their dimension to Earth, or it will show some initial battle of no consequence from before they meet Kaito in episode one. No combined mecha though, as Zenkaiser's gun is what makes them giants and I don't think he'll appear transformed in it.