I actually have had some strange problems myself. Not really sure if this mod is at fault though since the station I launched into space uses 3 different mods.
I built a large (unmanned )skycrane and welded it together (only welded the structure together, added the docking ports[from Konstruction mod], lights etc after) and I made a large space station out of welded parts, but again was careful not to use docking ports, lights, solar etc in the welds themselves. I launched it, made it into orbit, detached the skycrane and the station, with 6+ kerbals in it suddenly became debris that I am unable to interact with. I can set the ports on it as a target for my skycrane but they refuse to dock with each other again. I thought, maybe I shouldn't have welded the command pod to a habitation ring, so I tried again without using that 1 piece, just using the parts separately, but made no difference. Then I thought, maybe the ports are the problem so I quickly made a small 'tugboat/ferry' type piece and launched it hoping to connect to the station and make it usable again and for the first time since buying this game a few years ago I CTDed, as I got close to the station. Not really sure where to go from here, maybe build the whole thing again without weldments and see if it works.
Edit - I tested the docking ports and they seem to work fine, so I launched my second station attempt again, this time first manually re-rooting the entire thing to the command pod and this time when I separated it worked like it was supposed to. I have never used skycranes before because they were too wobbly when built to the sizes I needed, so I am not sure if its normal but I guess I can't use the skycrane as the initial control point with a command pod attached. I have to use the command pod first so when I separate in orbit it doesn't get assigned as debris? Either way this mod is working for me so far, never would have made that skycrane fly without it.