Once in a great while we see this issue with either bootinfo script or Boot-Repair which is running the bootinfo script.
Often related to file corruption. Did you have an abnormal shutdown, power failure or force shutdown? That can cause file corruption and then script cannot open a partition.
I might first try chkdsk on NTFS partitions and e2fsck on Linux partitions. I think Boot-Repair tries to run fsck on Linux but may not yet been able to. Yann knows details of his program.
#From liveCD so everything is unmounted,swap off if necessary, change example shown with partition sdb1 to your partition(s)
#e2fsck is used to check the ext2/ext3/ext4 family of file systems. -p trys fixes where response not required
sudo e2fsck -C0 -p -f -v /dev/sdb1
#if errors: -y auto answers yes for fixes needing response see man e2fsck
sudo e2fsck -f -y -v /dev/sdb1
And you only can run chkdsk from Windows, so Boot-Repair cannot run it. From Linux you can run some things that do very minor fixes to NTFS and set chkdsk flag so next time you boot NTFS it will run chkdsk.