Suppress the gear mate, rotate a gear to align it, suppress the gear mate.
If the gear teeth start off aligned and become misaligned as the gears are rotated, you may have a different sized teeth on each gear. Check the 'module' of the gear.
Could you upload the model?
The problem was with direction once I reversed direction they realigned automatically. I can give you the gears if you want
Gears are perfect their module center distance are 100% correct they were calculated using Gear Trax which automatically creates the gears
there will be lack of confinement of the gears, to prevent misalignment, after gear mates, sketch a circle on the hub of both gears and then mate these sketches with your gears as concentric. Maybe your problem get resolved.