Normally...microbubbles are caused by water vapor in the plastic. It can come from water vapor on your cup, air from the microwave (which seems to dry out over a couple reheats) or it can be picked up by leaving you plastic open to the air.
If you wash your cup, make sure you dry it really well...and then give it 20 secs or so to drive the water vapor off.
However, I've been doing some testing and another cause of microbubbles can be due too the plastic not being completely mixed.
If they are really big bubbles...you may have mixed them in by stirring the plastic to aggressively or by shaking the plastic (vs a mixing type motion).
My final observation is...funny how we get very few posts on microbubbles during the winter....and as soon as spring rolls around....!