Hi DrBombs, thanks for posting your .3dm model file.
I took a look at this curve in it:
I tested extruding it and filleting it:
I closely examined the partial fillet results and I could see there are some small fillet fragments in these 2 areas here:
Here is a closer look at the top one:
So why are there small fragments in those 2 spots? The reason is that those are the only 2 spots
where the connecting curves you made are not fully smooth to the adjacent segments.
If you zoom in to the top one you can see that it's not smooth here:
Filleting does not like it if you have 2 surfaces that come close to being smooth to each other but
are actually slightly creased. For filleting you want to have either everything fully smooth or fully
sharp and not something halfway in between. That's because at places where surfaces meet up
at a crease the fillet surfaces have to be extended and intersected with each other and that's one
of the most complex areas of filleting.
The easiest way to fix it is to actually do less work and don't put in any of the small connector pieces at all.
Instead let the filleter round off those at the same time it is filleting everything else.
That's far more reliable because the filleter will be able to make corner juncture patches where
fillet pieces are meeting up and won't have to do extensions and intersections.
So for example with this shape it's easiest to set it up like this with all sharp corners (.3dm attached) :
Then extrusion and filleting of this type of structure will be much more reliable:
The reason why is that it allows these juncture patches to be formed:
When you manually put in all the junctures in your base curves, it's a little different structurally. You're making
it so fillets have to be built around those pieces instead of being able to place them in itself.
There can be other situations where it's good to kind of pre-fillet curves but it's more for situations with
more complex surface arrangements, but for filleting extruded pieces with just flat end caps it should be
best to not pre fillet them and allow the filleter to do it.
Hope that helps!
- Michael