The problem is that NASA wants two open ports when you attempt to connect. So there is primary CBM (earth facing Node 2), and backup CBM (sky facing Node 2). They are rearranging the station so that the up-facing CBM will get PMA-3 + NDS interface attached and will be PMA/docking backup. And MPLM will be moved from Node 1 earth facing onto Node 3 (forward facing port), freeing up the CBM as backup.
You can see a lot more about this and the reconfiguration in this question and its answers.
So if a crew vehicle is on station using PMA-2 (forward facing Node-2) then could a cargo dock to PMA-3? And would that mean the cargo vehicle has no backup if an issue with PMA-3 occurs?
This is true if SpaceX bids Dragon V2 for cargo as well. NASA did allow in the RFP for PMA docking for cargo, but did not seem to address this issue.
The crew vehicle also serves as lifeboat so will stay on station 6 months or longer. Would that then block cargo vehicles from using PMA-3, or will this restriction be relaxed?
On the Russian side this is less of an issue since there are 4 possible ports, and one is almost always a Progress, so they could dump that if a port fails to allow the new vehicle to dock.