It may not be conflicting. GCMS notes is a system dump of their online tool. So it shows you all the status and their changes. The "Fee received" status would be on a later date compared to "Fee outstanding" status. The statuses I think are listed most recent to old ones. You should be able to see dates when the changes to status happen.
In general, look for case analyst notes which should be towards the end of the notes where case analyst makes notes about eligibility, recalculation of points etc. The first page of your GCMS notes should show you the status summary of criminality, security check etc.
