To the east of Whiterun is a cave called Swindler's Den, it was also part of a side quest for some redguard woman. Been through it three times now and it still doesn't show as cleared? What am I missing, I believe I have found all loot etc... Lydia was killed there on our first visit, I'm wondering if that could be the reason why it's not clearing?

Any help appreciated, cheers.

did you kill the redguards in there? i have the same issue, and i think its because i sided with them and let them live.

I have killed them, but like you I also sided with them first.

Siding with them causes this sometimes.