"You might try importing it into a different CAD program which has a more robust fillet engine like ViaCAD or OnShape."


I also had similar problem but also often running in some fillet issues mostly not wanting to
fillet at all not because of bad model but the fillet just don't want to do it's thing + it can be very slow.

When i saw how fillet works in Fusion360, it's just unbelievable what it can handle like "t-sections" or self intersections to name some.

I really hope that Fillet is on the priority list of Moi3D v4.0 - to make it way more robust and fast as possible.