It is common, in many of the Cisco Express 8.5 environments we have looked at, for the Total Incoming Calls given on a Traffic Analysis report to be a higher number than an Application Report.
The Traffic Analysis Report counts every unique sessionID (unique call) that is inbound (contact type of 1). The Application Reports do a similar thing but qualify (filter) only the records that have an application assigned.
There are simply times where inbound calls have been directed to an "agent" without having an applicaiton assigned.
The best thing the reporting user can do is to run a query on his or her database such as:
select * from ContactCallDetail where contactType=1and startDateTime > '2012-11-16 10:00:00' and startDateTime < '2012-11-16 11:00:00';
Usually when an application is not assigned to the record in the ContactCallDetail table it is because the destination type is equal to 1, which is an 'Agent' instead of a 'route point'.
So if you modify your select statement to filter by destinationType, you can quickly find the records that don't have the application assigned.
Example: select * from ContactCallDetail where contactType = 1 and destinationType = 1 and startDateTime > '2012-11-16 10:00:00 and startDateTime < 2012-11-16 11:00:00';
When you look at these records, you will see the agent that took the call from the destinationID field. The number in that field should match up with the field called 'resourceID' in a table called 'resouce';
Example: select * from resource where resouce=6011; where 6011 was the number you found in the destinationID field.
If there is still confusion about the source of the call - then talk to that agent and find out what is was.
Good Luck and let me know if you need further help.