When Windows defender scanns its own directory then each files are double scanned at same time and this cause high usage of disk with more CPU usage. I have trid explaining about msmpeng.exe proccess earlier and it is related with Windows defender.
How to find if Windows defender is scanning itself
In case if you don't know whether Windows defender is scanning itself or not then you can use proccess monitory from Microsoft to checkit.
- Download and extract process monitor (hardly 1mb in size)
- Run Procmon.exe
- Now find "Msmpeng.exe" from the list of processes.
See the path if any proccess with Windows defender have their own path then it is scanning its own directory and exclude directory from Windows defender setting.