This is a (relatively) common issue, at least on my SKR. It happens when the Z lead screw stub hits the top of the XZ plate slot before the Z limit switch is triggered.
It could happen because the limit switch on the offending side needs some adjustment (so that it triggers at a lower position), or it could be that the switch is being triggered but the SKR board isn’t recognizing that it is being triggered (aka SKR endstop issue).
I would start by manually triggering the switch during theZ homing to see if the travel stops correctly. If so, then adjust the switch 2-3mm lower (or bend the switch arm to contact the XZ plate sooner).