I have been getting that problem as well ever since I have formatted my shared partition of my internal drive to exFAT. Sometimes when turning on my MacBook or after a restart the partition would become corrupt! When I open Disk Utility it gives me a message that the disk cannot be repaired. I cannot access or recover any of my files on that partition. I routinely backup the files on the exfat-formatted partition as a safety measure.
Sometimes when I scan the partition with Disk Utility the partition would become corrupt! I get this message from Disk Utility.
Verifying volume “disk0s3”
Checking volume.
Checking main boot region.
Main boot region is invalid. Trying alternate boot region.
Checking alternate boot region.
Alternate boot region is invalid.
The volume could not be verified completely.
Error: This disk needs to be repaired. Click Repair Disk.
Verify and Repair volume “disk0s3”
Checking volume.
Checking main boot region.
Main boot region is invalid. Trying alternate boot region.
Checking alternate boot region.
Alternate boot region is invalid.
The volume could not be verified completely.
Volume repair complete.Updating boot support partitions for the volume as required.
Error: Disk Utility can’t repair this disk. Back up as many of your files as possible, reformat the disk, and restore your backed-up files.
I cannot go further than a week without the exfat-formatted partition becoming corrupt. It is very irritating. This is the only way to have a partition format that I can access with both Mac and Windows without relying on any third party drivers.