The Hot End nozzle can cause this problem if is have the throat Teflon tube inside that has melted from the throat.
In the attached Image the Nozzles has part of the Teflon tube melted into them this causes under-extrusion.

Nozzle & Throat.jpg

Proper throat cooling will prevent this, I have added a 2 fin heat sink to the throat.
Further modifying the model cooling duct to cool the throat.
Sensor.jpg


This is not limited to just the nozzle the Teflon tube in the throat can become deformed restricting the filament movement into the nozzle.

This will only apply if the throat in your 3D Printer has a Teflon tube inside.

Throat.jpg