I have the same plane/Trainer and never saw any bubbles.
No bubbles while running is fine but on mine the fuel does not run back.
Maybe a tiny air leak???
Also on another thread I saw where the adding a fuel filter helps with any foaming of the fuel.
Sure it wasn't foam?
Because foam and bubbles would go to the top of the tank and your drawing from the bottom.
Next time don't shake the plane.
Before you start it choke the carb with your finger and turn the prop by hand.
It should suck fuel up the feed line with no bubbles.
If you see any then perhaps you may have a tiny air leak where the line draws from the tank.
Just giving my 2 cents on what I just did here.
PS: What brand fuel??