Why did Emsisoft Scanner flag a safe file as malicious?

Why did Emsisoft Scanner flag a safe file as malicious?

Overview:
PUPs (Potentially Unwanted Programs) for example are flagged by our FileGuard protection during a scan. Some of these apps are harmless and therefor first need to be submitted to our lab, the same way like an app flagged by our Behaviour Blocker.
See instructions here. 
Then they have to be added to the Scanning Exclusions, otherwise it will be flagged again each time it is updated without the necessary certificate.
It can also be a known False Positive that is flagged. In order to have immediate access to that .exe, one should still submit it to our lab, but can afterwards restore it immediately and then add it to Scanning Exclusions and also to Monitoring Exclusions.

How to add a file to Scanning Exclusions:
Open the Workspace, click on: Protection Policies and choose the desired Policy Group. Then scroll down on the right till: Exclusions. Under: Exclude from scanning, click on: Add file or Add folder and and add the wanted exclusion/s.

This list also displays the path of any files or folders that have been excluded from signature based detection by the Scanner and the FG.

An exclusion can be easily removed at any time by clicking the Trash can icon.