Was your management done via Vlan12? If so...that would be a problem.
Ideally if you want to remove a VLAN from a port channel, you remove it from the port channel interface. This will then propogate down to the physical interfaces.
If you remove it from the physical interfaces first, your port configurations will no longer match the port channel interface configuration, and the ports will be unbundled. Typically this results in one going into blocking via spanning tree.
VLAN 12 was not the management vlan. It just was an old vlan that needs to be removed. VLAN 2 was the manegement vlan and was configured on the trunk. I believe your second point should be a valid reason for it. I should have removed it on the port channel before moving to the individual ports.