Is this a membrane protein? Membrane proteins commonly have a dip in that region, due to some influence of the micelle. For a very high resolution membrane protein which is cleanly classified, the dip will get smaller, but usually doesn’t go away entirely.
As mentioned previously, too tight masks can also cause these dips - I would be especially careful about that since you see such a big difference between the spherical and loose mask.
If you have a very sharp dip at higher resolutions than what you see here, like around 2 - 4, than defocus refinement may help.