You need to use fsck -f for a thorough check. This checks the filesystem even if it appears to be clean. You can also do this by adding ‘forcefsck’ to cmdline.txt to get the OSMC initramfs to check in more detail.
I’ll do that if it happens again. It’s running absolutely fine now so while it isn’t broken I’m going to leave it be. Thanks for all your help though (not just Sam but everyone on this thread) I have a better understanding than I did before!
Good time to take a backup! 
I will as soon as I get everything exactly how I want it. Need to wrestle with Samba and OpenVPN yet! 