Not bleeding all the air out will cause bubbles.
A small leak could let air in. "Less likely"
Is it an after market cooler or custom made?
I havent tried water yet, but I've been researching it and I think you need a radiator and a seperate reservoir to keep all the air out. Without the reservoir when you get evaporation you could get air.
Hopefuly its not bubbling because its boiling the water from being to hot. That would suck.
Im guessing you got in a hurry and didnt bleed it right. Sometimes you think you got it and there is a pocket of air hiding that shows up later.