Q: One visitor asked, "What causes air bubbles?"

A: Fish eye bubbles. You can get those in Oil modified finishes as well as polyurethane, and the reason is usually too rapid drying. The finish does not have enough time to flow and level before it sets up. I think that for any finish, prevent any sort of draft or moving air until the finish has leveled out. In the case of water based finishes, give it an hour and then ventilate the work area. It is interesting that you mention the finish you used seemed to vary from can to can.
It is also quite possible their was something wrong with the finish itself. That is not unheard of. You could be a magician, and no matter which way you stroke it, you can't make it bubble free. I have been there too. I will say that water based urethanes have come a long way. The top of the line finishes are cross linked (you add a cross linker). Very hard when cured but have certain procedural standards that must be followed in application.