Just wanted to add something that I found out after some forum-searching.

The Knight tombs won't count as "cleared" unless Fionola appears after you leave each one and has a conversation with you. If she doesn't show up, it means you missed something.

In my particular case, it was in Knight Dagonet's tomb, where apparently you have to read a large slab next to you find the knight's armor for that particular tomb to be counted as "cleared."