If the bubbles are "champagne bubbles" and no bubbles end up in the tubing, there's no problem. However, if you do end up with bubbles in the tubing, you have to try to stop this happening.
Different people have different methods of preventing bubbles appearing in the tubing. I had to try various methods and eventually found what works for me.
I heat the insulin to body temperature (by putting the vial in my bra). I then pull the plunger up and down the reservoir to "lubricate" it. I draw up air to the second last line in reservoir and push that into the insulin vial. I then draw up insulin to that line, push it all back into vial to get rid of bubbles and draw up the same amount of insulin again.
I then tap the reservoir with the top of a test strip container to get rid of bubbles. I tap, tap and tap, pushing out bubbles when they rise to the top. I hold the reservoir so that bubbles will rise to the top.
When I can't remove any more bubbles I remove the reservoir from the connector and tap its bottom on a flat surface to try to get excess air up to the top.
Then I attach the tubing, push insulin into it and tap reservoir again to try to remove more
air. I repeat tapping and pushing the plunger until I've got rid of all the air I can. Then I place reservoir in pump. I am now free of the huge bubbles I used to get in the tubing but sometimes still get tiny ones.
I hope this is useful - it's actually a combination of different tips from DSN, Medtronic rep and another forum. You might not need to do all of this, but you might have to do more.