I also am seeing the non-manifold edge here. Here is a quick model I did that has a working fillet. Since the extruded circle diameter is the same as the hole dimeter, the extrusion and the hole share a single edge that is of infinitely thin thickness, which can computationally break downstream features. I altered the circle diameter by 0.001 mm just so the intersection was no longer infinitely thin, and the fillet feature worked out. Please see the attached. Out of curiosity, I made a similar part in V27 to test fillet capability, but I ran into the same issue. If you happen to have an example where a fillet did work in V28, but will not work on the same geometry in V29, I would be very interested in looking at this.
Let me know if this helps.