Lots of things can toss you the micro-bubbles. As Lamar described, this is the way to fill the injector to help on bubbles. Here are some other thoughts:
*If you store your raw plastic where humidity is an issue, try keeping it in a room that's de-humidified and take only what you'll need for your injection session to your work area.
*If you are shaking or stirring vigorously to re-incorporate all of the components of your raw plastic, let it rest for ten minutes before using it.
*Washing and drying your cups can help get any film or contaminants off of them that might offer a place for moisture or air to hang on un-noticed.
*Pre-heating your cups in the micro-wave for 10-15 seconds, then wiping out with a clean dry paper towel before mixing your batches is a good practice to develop since glass and cool raw plastic being heated at microwave speeds can create air pockets.
*Before you start each session, try heating an empty cup in the microwave for twenty seconds, remove the cup and wipe down the interior surfaces of the microwave cabinet with a clean paper towel can help eliminate any heat related moisture that can transfer to your plastic.
*Before I mix the first batch of plastic I re-melt a cup of old, junk plastic and do my plastic/colorant shaking while the plastic melts and gets to about 360 degrees. I suck up an injector full, then stand the injector full of the plastic upright [nozzle up] in a corner where it won't fall over. This gets the injector hot and all parts heat expanded so the injector itself is not going to be at issue. While the injector is heating up I put the cups I'm going to use in the microwave and do the heat thing, then wipe the cups and in the interior of the unit.
*I keep an extra set of rings handy for each injector I have. I have never replaced a ring in the primary injector I use and have been using it for over 8 years without an air or serious bubble issue. I cut a ring putting a nozzle back on in my twin injector so I replaced all of the rings so that everything would be operating in unison. In my opinion the injector's rings are seldom the source of bubble issues.
When I first began this plastic injection lunacy I was seeing the thin lines of very tiny bubbles that seemed to run smack thru the middle of my baits once in a while. I too got nerved up with them but finally just let them exist for a couple reasons. I like using hi lite powders in my mostly small and very transparent Crappie baits. Hi Lite powders go to work on the bait's exterior surface. They also work in reverse by affecting the surface of each of those tiny bubbles. Its a double whammy in the light reflection department starting with surface reflection and then from the interior as the light passing thru the plastic hits the bubbles. Its subtle but its also close to identical to how light works on some natural baits. Sometimes a little bubble action works for you instead of against you. ...just something to thionk about.