Hi Rogurt, thanks for posting the part, that really helps a lot to figure out what is going on.

Just to help clarify, Steve above is referring to these areas of your model here:



Those are areas where the 2 surfaces come to a shared tangent instead of having a distinct sharp crease. That can definitely be confusing for the filleter, because it's a "disappearing fillet" situation, the fillet between tangent spots is non-existent.

If you want these areas to be all straight like this:



You may want to instead create some larger sweep areas like this or something:




Here's another example to help illustrate what the fillet would be trying to do in your case - here I've built a surface that has a steep angle to the other plane at the sides and in the middle it dips down and gets flatter to the plane approaching that kind of shared tangent situation like you have:



When I put in a fillet there you can see that in areas of shallow angles like that the fillet gets smaller and smaller:



And in your case the shapes are much more tangent to each other than what I show here.

Basically the kind of shaping that you have there creates a sort of anomaly in the fillet right in that middle area.

- Michael