This is probably very easy to use on windows, but i could not find a windows machine,
A quick solution that was not very clear at first was as follows, before you do this, make sure you have unmounted the SD card !
apt-get install exfat-utils
And then run the command
sudo exfatfsck /dev/mmcblk0p1
Got a few of the following error, and answered yes to all
ERROR: unknown entry type 0xc1. Fix (Y/N)? y
And that was that