LE10 and earlier use NTFS-3G via FUSE to mount NTFS drives. LE11 switched to new(er) in-kernel drivers so you'll see a significant increase in file read/write performance. However the in-kernel drivers appear to be a little more enthusiastic about flagging issues; hence the change in behaviour that users are seeing.
LE normally does fsck before mounting drives but there is no fsck.ntfs utility to do this (ext2/3/4 etc. use /usr/sbin/e2fsck). In the past there was an fsck tool from NTFS-3G and I'm wondering if we might need to restore the package; not to switch back to the older driver, but to build and pick the fsck tool to the image.
Kodi allows drives to be selected and unmounted in the file browser, but otherwise the GUI doesn't have an easily accessed option and you'd need to create an unmount-all script and then map the script to a custom remote keymap.