That's the recommendation, but what it really means is that it's recommending using First Aid in Disk Utility that's not on the boot drive. It could be from recovery (which is a volume on the same drive but not the same partition), Internet Recovery (which loads recovery mode from the internet into main memory). Another way is to have a bootable external drive and running it from Disk Utility but on the internal (now non-boot) drive..
The other thing is that often using First Aid doesn't help if the issue is more serious than it can fix. I've seen a few cases where it recommended that and when I checked with First Aid it was complaining about the same types of errors and recommending running First Aid from Recovery again.