I'm seeing the same thing, although the vessels are destroyed (well, completely disappear actually) no matter which docking port I click on when I decouple via the parts manager.
One difference, is that I strutted the lander and orbiter prior to launch to reduce the dreaded wobble, but can't find any way of removing the struts after launch. There's nothing like KSP1, where you can right click on a strut and remove it - parts manager doesn't have that functionality.
I guess it's possible the struts combined with the two docked vessels are causing the 'destroy' bug when I try to decouple.
Sigh...