I keep getting this error every time I poweroff/rebbot my computer. I've everything installed on LVM except /boot.
I'm worried if this will affect the data on disk.
This happens because you have your "/" partition located in a LVM Logical Volume inside of a LVM Volume Group. When your system reboots or shuts down one of the last tasks is to unmount all of the volumes to prevent data loss. In the case of LVM this is impossible becasue the "/" logical volume is technically still in use, so you will recieve a warning like "Could not deactivate volume group "NAME" with 1 logical volume open". In this case the Logical Volume that contains your "/" is preventing your Logical Group from being unmounted because it's still being used. I for one have not see any issues with this behavior, however that doesn't mean there isn't any. If the issue worries you, optionally you can relocate your "/" partition outside of the volume group. This should clear the error message your recieve.
Hope this helps