What you experience is temporary under-extrusion. This could be a typical result of friction in the supply of filament to the extruder. I've run into this also a week ago when the shaft of the spool holder caught a plastic bag next to it which wrapped around the shaft creating a lot of friction. Friction can also be caused by filament that gets entangled on the spool, this is usually a problem if the spool unrolls too freely on the holder (too less friction);it unrolls a few windings, and then tightens those entangling the filament. Also, if you use 2.85 mm filament on small diameter spools, the last stretch of filament has the smallest curvature and as such requires the most force to pull it to the extruder (this can go in steps).
Furthermore, slipping of the extruder gear is also a (rare) possibility (when using a stepper directly to drive the extruder gear, a flat spot on the stepper shaft should prevent this).
Be sure to inspect the filament release from spool to extruder and try to see (and listen!) what happens when you print a part when you experience the under-extrusion.