Microbubbles are usually moisture...as I've read on the Forum a few times, and had suggested to me by a few Members, nuke Your cup for about 30-45 seconds before You put plastic in it. This helps. The larger bubbles...if You're getting the bigger bubbles with remelts, air may be left in the mix from pockets between the Plastic Chunks that were cut/chopped up to be remelted...or if it's new plastic, it may be possible You whipped air into the mix(?).
It may be Your injector not sealing right, as has been mentioned.
When I get the bigger air bubbles, especially with remelts, once I get the plastic upto temperature/viscosity, I let it set still, not stirring, not drawing into an injector...I'm giving the bubbles time to come to the surface. Add a little Heat Stabilizer for this. I may lightly reheat 2-3+ times, using my stirrer to "move the bubbles out of my way" on the top of the melted plastic, until I see bubble-less plastic...time to shoot.
(This is On Me since I started typing)...Then I stick the tip of the injector in, kind of deep, and draw slowly so I don't suck air down into the plastic...and keep slowly lowering Your injector as You draw, keeping more "distance/length" between the Injector Tip and the top of the Plastic Melt. Watch the top of the plastic...You can suck air into it with the force of Your injector, and as SOON as You do, that air will be in Your injector.
Then inject pretty slow...if Your mold cavities have alot of details, not smooth like a Carrot, shoot slow.