Do you mean the bubbles that appear on the side of the tank when you very first add the purifer and the eggs? Those bubbles will dissappear after a few days, then the water will basically look 'clear' (allowing you to see the sea-monkeys better) so even though the few actual bubbles that the pump creates almost immediately disappear, you're doing it right by just giving them around 6-10 squirts a day. :-) My sea-monkeys get stirred up as well, but they don't seem to mind. You can oxygenate slowly, that works just as well!
Hope that helps. :-)