Hi Matt - the difficulty here comes because you're only filleting some of the edges and leaving other ones unfilleted. That then makes a sharp abrupt meeting point between the fillet pieces and it becomes difficult for the filleter to deal with intersecting the pieces with each other.

The difficulty is because of the different sizes of the fillets - the fillets are made up of arcs of the same radius but because the surfaces meet at different angles the arcs are of different arc lengths for the different fillet pieces.

Here's a zoomed in screenshot trying to illustrate this:



The fillet pieces that will be created for these edges will look like this:



So you can see there how those fillets are of quite different widths which will abruptly kind of slam into one another. It's difficult for the filleter to figure out how to trim these things with each other. Usually the solution is to also fillet the other side edges at the same time, that will allow the fillter to form a corner juncture patch at that area which gives it some room to deal with different sized fillets coming together.

But the normal solution to fillet all edges won't work very well on your particular model here because of this little tiny edge in this area here:





That's also not good for filleting to have such a small edge in part of the object structure, another thing that's not so good is to have several different surfaces that are only at very shallow angles to one another like your back side of the object has. Instead of having several surfaces meeting very shallowly there it would be better to have just one slightly wavy surface as in the attached 3DM model file, where I sliced off the back side with a side profile curve to make just one large surface on the back rather than 3 shallow angled surfaces. Now with the attached 3DM model file you can fillet those side edges as well and you will then see a result like this:




So notice there that with the side edges included in the filleting the pieces don't just abruptly collide into each other like your original case would force to happen, instead there's the fillets are able to be stopped a little bit before they run into each other and a corner juncture patch put in between them, that will usually give the fillet a better chance at working than one that tries to retain some sharp edges where fillets meet up.

If you don't want the back side to be filleted you'd probably want to make a selection like this:


then you'd get a fillet result like this:


Hope this makes sense,

- Michael