You are correct - the use of an intuition point at a crime scene will highlight all items that you have not yet gotten clues from. (The LA Noire Wikia seems to back me up on this.)
However, it may highlight items that you've previously examined but have not yet discovered a clue from - for instance, there are several items in the game that you can rotate, open, or otherwise interact with in order to find more information. I think it's likely that you need to continue to examine the highlighted object to get another clue.
For instance (possible spoilers ahoy if you haven't 100%'ed the Traffic Case "The Driver's Seat"):
At the Black residence, there's a photo of Adrian Black on the dresser. This in itself isn't all that interesting, but if you flip the frame over and open the back cover, you'll see a message from a woman named Nicole on the reverse. The photo is not a clue, but this concealed message is.
Of course, it's also possible that the highlight on the object is a bug :)