Kerbal Space Program

last thing (sorry) my only mods are kerbsl engineer and quantum struts, but these shouldnt affect anything

Navball markers are oriented to the choosen direction to control.
This is not a bug, but a feature request IMO.

Navball markers (prograde/retrograde) always correspond to the ship's movement in space, relative to the selected reference frame, i.e. the planet's inertial frame, planet's rotational frame, or to target. That direction does not depend on center of thrust and there's no need to change it.

The center of navball, denoted by the --v-- icon, is pointing in the control direction of the selected control point. It may be a command pod, command seat, probe core, or docking port. Navball does not follow center/direction of thrust, never has and never was intended to. For many maneuvers, particularly docking, or when using engine groups as RCS replacement, such function would be annoying and uncomfortable. It might make sense to be able to have "control from here" option for engines but it is a new function, and it does not have much parallel in real world - direction of all kinds of navigation instruments in real spaceships also does not change with whatever engine is ready for use at the moment.