Hi Sharon,
Any time I've indexed in InDesign, I found that I have to proofread it before even generating it, and then of course after generating it.
In my opinion, it's wise to look at all the Index entries in the indexing palette for all the files in the book first, then generate, and then proofread (at least twice!). [not to mention that InDesign doesn't know how to alphabetize.]
Yes, sometimes things show up in InDesign that might have been there in Word (doh!) or even accidentally put in with some keystrokes in InDesign.
And if you're only looking at "hidden characters" in InDesign, any overlapping index markers (two or more in one place) aren't obvious.
Hope this helps!
-Karen