I am running an ubuntu headless PC for Ekos and that has happened to me too.
Solution, make it run fsck at every boot. If it's ok it only takes a few more seconds, if it's not it will correct the filesystem by itself.
I know it's not ideal for an SDCard based system (more wearing of the card) but it's a solution.
Use this: sudo tune2fs -c 1 /dev/sdX, where sdX is replaced by the SDCard device.