I have been working with Zoho Support on an issue with the new Reports module. It is a wonderful upgrade to what was originally there. Unfortunately, there is a pretty major bug in it.
If you have a parent module with an inclusive relationship to the child module (always return a parent record, regardless of whether a child record exists or not), and you have deleted records from the child module (they are in the recycle bin), those deleted records are also being returned in the result set. Reports are, effectively, surfacing deleted records.
I consider this a severe defect, as the only workaround is to empty your recycle bin. I got a generic "we will be fixing this in one of our future updates" message, but it has pretty much rendered several of our new reports that we were able to build on the new Reports module useless.
Wanted to put this out there in case anyone else has the same issue. It's a known defect with no ETA.