Microsoft Safety Scanner says it is finding infected files while running but when finished says no viruses or spyware found!

If the Microsoft Safety Scanner (MSERT) found a number of infected files during the scan but the final scan results indicate no malware was detected...this is normal behavior by many Microsoft Animalware Software but not very well documented by the Microsoft Security Team. It is not unusual for Defender (or other security software) to suspect and warn about possible threats during a scan (a preliminary status indication) but later determine the file(s) were not an actual confirmed threat(s) upon completion. 
 
I explain this behavior in more detail in Microsoft Security products indicates detected files during scan but does not show anything after completion (Post #22).

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The Microsoft Safety Scanner works in a different way to other anti-virus software, during the scan it marks files that may be infected, and at the end of the scan, it tests them against the malware database, if at the end of the scan it is indicated no problems were found, then your system is malware free.