Your technique for connecting straight lines with arcs is producing small tangency errors which causes the filleting to fail. Use the curve Fillet command to connect two straight lines with an arc segment. Fillet will do it correctly with no tangency errors.
The easiest way to determine where your arcs are not tangent is to examine where fillets are failing. Mark those locations using dupborder and then delete the failed geometry and go back and replace the arcs in the curves where failures occurred with curve fillets of the same size. Then try the extrusion and filleting again.
FixedCurves.3dm (164.0 KB)