I have not been able to narrow down what causes this, but most of the time after i use connector ports to transfer resources around one of the ports are stuck on the craft, and i get this message when trying to remove it.
http://images.akamai.steamusercontent.com/ugc/46506585708886650/2599F1C362D8F4AEEC71CF9EECB696D90E12450E/

"Part cant be grabbed because 1 part is attached to it"..... is this just something I am doing wrong, for as often as it happens to me, I have not found any mentions of it... :(

I've not had time to test extensively, but I've been experiencing the same issue, and so far it seems to be the connector is break the link from that I end up not being able to remove.

I imagine that, upon disconnect, the child vessel has its root part reset to the connector port, as that would have been the closest part to the root of the combined vessel before disconnecting.

I think space-is-hard is right, the part become the root on undock.
Anyway, I changed the way attach & detach work in the next version of KIS (1.2), so this problem will no more happen ;)
Also it's a KIS issue, so I'm closing this report.