Hi Josh, the thing that's probably causing fillet difficult in those areas is that this cutout surface here is not smoothly closed, it comes to a slightly sharp corner where it comes together:





When there's a sharp crease at an edge rather than a smooth closure, it means the fillet surface that is created along that edge also does not close smoothly with itself either and it becomes much more difficult for the filleter to figure out how to deal with that.

Ideally you'd want to have made those surfaces used to cut out those areas smoothly closed and then there would probably not be any problem filleting those things. It can be difficult to go in later on and try to fix stuff like that up, I'll take a look though.

Anyway that's what's likely to be the cause there - filleting especially does not like it when things have sharp creases like that but with it being fairly close to being smooth but not actually smooth. It tends to mean there is a pretty tiny slivery gap between the ends of the fillet surfaces that are generated along those edges.

- Michael