I was having the same problem with a Font Collection that I created a while ago in Yosemite and migrated to El Capitan (not sure if that makes a difference). Anyway, it wouldn't let me add any fonts to it.
Booting in Safe Mode and restarting did nothing for me. Eventually I just created a new Collection and deleted the Collection that was giving me problems. Everything seems to be working fine in the new Collection now.
I also deleted the Font Book preferences, as suggested HERE. I did this after messing with the Collections, so I'm not sure if it made a difference. I'm also not sure if this is any different from what Safe Mode does, but it's worth a try…
Close Font Book and go to the folder "username"/Library/Preferences/
The file you delete is called com.apple.FontBook.plist
If you're having trouble finding the folder go to the Finder, click 'Go' in the menu bar and with the menu open press the alt key to reveal the Library folder.
Once you've deleted that preference file, restart Font Book and it'll make a new preferences file (don't worry, you won't loose any of your fonts or Collections by deleting that file), and hopefully it'll be working again!