Hi Brian, thanks for posting the model, that really helps to see what is going on.

One thing that is really going to mess up the filleting in this situation is the back edge of the wing which already tries to come in kind of smooth to the main body, it is at a very very shallow angle, kind of practically pre-filleted already:





When you want to set up something for filleting, it will actually tend to mess it up a lot if your surfaces are partly blending together as if they were filleted already, that's kind of what you've got in the above situation.

Instead, the spot that you want to fillet should have the surfaces meeting at more of a sharp crease, kind of a more distinct edge rather than partially smooth already.

More like this for example:



Then fillet will work a lot better on the more distinct edge:




Basically if the edge to be filleted has surfaces that are already partially smooth together, that creates a difficult situation for it.

So don't try to make it so smooth initially, you can make it approach it somewhat but not to the degree at the spot where I showed above. Instead let that area be more of a sharp edge and let the fillet smooth it out instead of trying to build it partially smooth already.

Hope this helps!

- Michael