Hi Alex, I'm sure it's some kind of bug in the "intersect with side faces" step of the filleting process.

One thing I noticed when examining the surfaces is that they are generic cubic spline surfaces with 4 points in one direction, note this when turning on control points:



So that means that operations involving those faces are not able to go through any special case plane handling which usually will improve accuracy.

I tested replacing those 2 surfaces with simple 4-corner-point planes and that seems to then work better, see attached file. I replaced them by deleting them one at a time and then selecting the object and running Construct > Planar to fill in the planar hole.

How was the shape originally created? Because all the edges that look like lines are not simple lines but generic cubic curves now, is this the result of running Flow on an original object? The downside of Flow is that every surface and edge in the original object is going to get turned from an analytic curve into a generic curve so that it can be potentially warped into a different shape. This may be degrading the analytic quality of your object if you're doing this often.

I don't particularly see anything actually wrong with the object though, it may be possible with a lot of detective work to fix Fillet to work with your original.

- Michael