When you select the boundaries/edges for fill they may contain sharp points/vertex(i.e the edges are not smooth curves) between end to end at many places. when you apply fill the vertex tends to bulge forming the bump/deformation.
You can optimise the fill by first applying curve smooth to the Edges/boundaries and then apply fill command to patch surfaces. Bump still will be present if the curve is not completely smooth.(i.e if you are not able to erase all the vertex of the curve and make it smooth).
You can use supports option to still minimize the bump.
Have a nice time.
Thanks for the info. but it seems it a bit more confusing to smooth the curves out. But I will continue to try to smooth them out. Thanks for the help.