I ran into this issue in my own environment recently. In my case, I was trying to remove a provider VDC, which has a single org VDC inside it. The vApps had been moved to an org VDC under another pVDC, but vCloud wouldn't let me remove the pVDC.
The organization network was shared between both VDCs, but there wasn't any way to "unshare" it from a VDC.
I ended up having to reconfigure all the vApps, and delete all their network configurations, in order to remove that organization network.
I think this is what the OP was experiencing - this inability to unshare the organization network.