I would reduce the retraction distance to something like 1mm. Cura defaults to a high distance value since Ultimaker uses a Bowden extruder that requires it. 1mm to 1.5mm should be adequate for most filaments on a direct extruder. If I understand the min extrusion before retraction setting, the default of 0.02mm seems awfully small. Combined, the settings will reduce the number of times retractions can cause the same section of filament to be rolled past the hobbed bolt.
BTW - my settings are being used with 1.75mm filament. 3mm could require something different, if that's what you have.