OK so the specific issue we're addressing here is the one @shoopi posted above where you do a scan, the status says you have some issues but the issue list says "Congratulations you have no issues" in green.
We've found the bug and it is:
If you're doing a scan and you have comment scanning for malware URL's enabled OR "Check password strength on profile update" enabled. Then:
If during a scan someone posts a comment OR someone updates their profile, your list of new scan issues will be deleted up to that point. So if the scan is halfway through and it adds a few more issues you will get a partial list or you may get no issues at all which seems to be more common.
The fix is to disable the following two options at the bottom part of Wordfence options page under Other options:
DISABLE Scan comments for malware and phishing URL's
DISABLE Check password strength on profile update
This is a TEMPORARY fix and the next version which will be out in a few days will have a permanent and proper fix.
Regards,
Mark.