Any ideas what's going on here? Top and bottom pieces were printed side by side but only the top piece is effected. It's inconsistent as well and only does it after an hour or so into a print. I'm leaning towards temperature control...?
I had a similar problem and found that it was caused by too large a retraction for the travel between the parts, so reducing the retraction distance improved the issue.
Large retractions can cause air to be drawn into the melt chamber (unlikely) and disturbing the flow temporarily, also the act of reversing filament direction can cause a change in the filament profile due to filament stretching in the hotter regions of the filament path or the hob bolt (direct feed only) creating additional grooves/distortion in the profile; this will cause small changes in flow rate; filament being drawn back is warm so more easily deformed unless you have a well cooled cold side before the heat break.
Lastly, periodic changes in filament dimensions during manufacture will also cause what appears to be starvation issues. Retraction can be a compromise with some filament types, colours and diameters and for 3mm filament can be worse, so choosing a quality filament is important.