We've seen something similiar in our orginal testing, all you need to do is uninstall the VC 2.5 Agents from the affected hosts, usually a rpm -qa | grep vpxa and rpm -e <pkg> and once the agent has been removed. I would suggest in disconnecting them from VC. Once disconnected, just reconnect to the VC 2.0.2U1 and it will drop the agent for that version onto the host.
FYI - One reason you could be seeing issues, is that your ESX have to be a certain patch level for 3.0.2 before you can attach them to VC 2.5 else you'll have all sorts of issues. This has been a documented issue on VMware I believe, but you can always open an SR and provide them your current patch level of your hosts to see if there is a conflict.
