I've never paid much attention to bubbles in the trans fluid or any other places - no offense to anyone but there are a lot of "old wives tales" floating around the automotive world.

If the fluid is at the proper level, and a nice healthy red, and the transmission shifts well and works properly- are you really going to take it to the transmission shop and tell them that you have "bubbles in the fluid?"

The rebuild place that said that bubbles in the fluid are a sign of bad seals and could cause the tranny to need a rebuild, or whatever - that sounds absurd coming from a certified (hopefully) transmission rebuilder. Certainly bad seals could -theoretically- damage the transmission if you let the fluid run low and continue to drive - but I have had old vehicles that I drove FOR YEARS with bad tranny seals and just made sure that the fluid level stayed up. The transmissions themselves worked fine the whole time. I even did let them run low when I forgot - if it don't go into drive then you need more fluid! But blaming a transmission failure based purely on the fact that there were bubbles in the fluid, that is just plain ridiculous.

PS - Overfilling the transmission usually just results in leakage around the fill tube O-ring, or possible damage to a seal that was weak anyway. If it had no way to get out of the trans then it could possibly mess it up, but most transmissions either have a place for the extra fluid to come out, or else they will just leak at one of the seals until the fluid level goes back down to normal and then stop - usually the fill tube seal.