A couple of things…
When you have too much negative pressure, the vacuum can cause air can seep back in behind the plunger seal. And a wider syringe barrel - like the ones that come with the omnipods - can create more of a vacuum because you would have to pull it slower to allow the pressure to equalize, compared to a narrower barrel.
Additionally, the plunger seals on the omnipod syringes are kind of cheap. So more air can sneak past them.
I don’t use the normal syringe, the one that comes with the omnipod. Because it has a much wider barrel, when you pull back quickly it creates a vacuum, and air can seep back in from behind the plunger.
Here:
I find those bubbles to be horrible with the omnipod syringe. So I always use a regular 100 unit syringe. They are cheap.
The BD ones are very good. Buy a pack of these and try them out. Only about $5 for a pack of 25.
https://www.amazon.com/gp/product/B0170PGQRI/
So that 
is the first thing to try.
I’d suggest trying those syringes for a month, and just see if it seems like you are getting less bubbles. After you get comfortable with that, then I’d suggest trying the negative pressure in the vial.
I am not 100% percent sure who else it was here who stopped using the omnipod syringes, and had better success. @Aaron maybe?
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