Myself, I would rather have one huge air bubble than a tiny one. A big air bubble can be easily fixed or altered for a custom project. Small holes mean a lot of work for little compensation. In most cases its probably easier to throw the cast away and simply make another. When dealing with tinted parts, its particularly problematic.
But "IF" you can manage to match the tint or are dealing with a standard color resin, the best way that I have found to fix a air bubble hole in a cast is to build up a small wall around the hole with clay. Then fill it up. You peel away the clay and a little bit of light sanding and Viola.
Of course, if the bubble is in an extremely sensitive or high detail area, it might be best to just make a new one.
If the bubble is in an unobstructed part of a mold channel, then cut out te bad area, reseat in mold and finish filling the mold. This method works great for making multiple color custom parts.