The rule books specifically state that the missions from the base game are not compatable with the second and third game areas, and the second game missions not compatable with the third. It says so right on page 2 of each booklet. If you ignore that and shuffle them all together it become quite unfair on the people stuck drawing the cards with limited available locations.
The games are designed to work together, but, as with any game where expansions are designed to work as both expansions and standalones, it never works perfectly. Cards keying off newly introduced mechanics have to be limited to avoid swamping the expansion when played as a standalone, but this means when the games are combined they become too rare. To repeat the best example: The scalable monsters are a great innovation, but since they needed to keep them to a reasonable level for TotG played as a standalone, when combined with the main deck they come up quite rarely.
This is not a problem unique to Anima, as I said it's common in any standlones-that-can-be-combined game. And the common solution is to release a Blender-style, non-standalone expansion, specifically to bump up the card numbers of the "new" types and other such tweaks.
The time travel thing was just me trying to make lighthearted conversation, and you appear to have taken the direct opposite to my intended meaning, which was that yes, it's not a big deal.