In the attached example I created a Tube and inflated one of its caps using Planar Inflate. Afterwards I colorized all polygons containing non-manifold edges to see where I have any problems. As you can see all polygons around the tubes edge where the cap has been inflated contain non-manifold edges. I guess this is, because Planar Inflate created new points instead of connecting to the points of the tube.

In the top level geometry parameter panel there are three toggle switches. These allow for different setups.

1. "Small/Large" toggles between a small and a large tube. This does make a difference.
   
2. "Union" I tried to use a union on the tube and the inflated cap. This solves all problems on the small tube but only some on the large one.
   
3. "Clean" My first approach was to use a Clean SOP. This has no effect on the small one and makes things worse if combined with union on the large one.
   

Is there a better way to repair non-manifold edges?