The dimples in pads are a consequence of the dispensing process and the adhesion of ink to the nozzle. They are formed when the nozzle pulls away from a finished pad, causing a small amount of ink to follow the motion of the nozzle for a short distance. We've tried out a number of methods in the past of smoothing out the dimples with different approaches (pulling gradually, in different directions, gradually reducing flow rate, etc.) but found that our approaches would either just move the dimple to another part of the pad (like a corner), or potentially impact either the infill of the pad or features closeby.
There are some ways of mitigating how pronounced the dimples are, though - reducing the print height to 0.6-0.8mm generally leaves a smoother finish, and burnishing will also smooth out the dimple. Also, touching up the component with the new solder will help produce a stronger joint, and allows you to adjust the orientation (just apply flux, add solder, and adjust component position, then hold in place until it cools).
In general, we recommend that any components that either must be held flat or will be in some way manipulated / placed under stress (like buttons, or potentiometers) are through-hole components and are point-soldered to the board. This will give the best joint strength and allow your components to be held in place. For components that will be placed under a lot of stress, @pathare found a great method of increasing the robustness of the joint by soldering out to a hatch pour - see his work here: http://community.voltera.io/t/reliable-through-hole-connections/263
We know that the little 'dimple' in the ink isn't ideal for some applications, but hopefully these suggestions will help with future projects.