In my experience with stacked walls, I've had similar issues and have resorted to "walking the model" in 3D like you are showing, and using Edit Join on each misbehaving condition. And then hope that the change does not affect another stacked join condition. On that particular project, I ended up "unstacking" the walls (select -> right click -> "Break Up") and then the joins behaved much better. Still had access to the stacked wall configuration (for placing, etc), but then broke it apart at the first whiff of problems.

FWIW,

Finish 1 [4] = exterior finishes
Finish 2 [5] = interior finishes

The numbers (in brackets) indicate the order of construction, structure is first, substrate next and so on... 1-5 (then there is structural deck)

An interior wall uses Finish 2 [5] on both sides of the core layer. An exterior wall uses Finish 1 [4] for the exterior finish layers above the core and Finish 2 [5] for the ones that are below the core layer.

Examine a stock Revit template's wall types and you'll find this logic is present.

That written, your issue is probably more related to stacked walls and how they join at different elevations than what I just wrote but if your wall types mix up this logic and some have finish 1 and some have finish 2...it could contribute potentially. Walls that span more than one level (visible in more than one level's plan view) and join with walls on different levels in different ways will create a paradox of join issues. They might look correct in the first floor but wrong on the next floor or vice versa. I try to find a way to separate the walls, mimic construction sequence, when this happens.