Unable to deselect items in migration-assistant
This posting seems to suggest it might be something to do with Server.app software - https://discussions.apple.com/thread/4157337?tstart=0

On the new machine, you might try removing Server.app from the /Applications folder and restarting. It might be that you need to remove Server.app from the backup before doing the migration - perhaps you can boot from the clone and remove it from the clone. Removing Server.app from the /Applications folder should cause the system to warn you that it will shut down all the server services, but should otherwise leave the server data and settings intact so when Server.app is reinstalled everything will be as it was before.

Server.app seems to also cause probelms with "not enough room" warnings that are incorrect but still prevent Migration Assistant.app from completing its job as detailed in Migrate OS X using Migration Assistant and Time Machine - not enough space