Identify the kind of bubbles that you have. If you have small bubbles, called "seeds," already exist in the wine bottles before you fire them, then there is little that you can do about them. Simply avoid buying glass with such manufacturing details in future. If you have large bubbles that sometimes break through to form a hole or small bubbles that form between layers of glass, you can minimize these defects.
Eliminate the large bubbles described in Step 1 by checking to make sure that your kiln shelf is even. Use a a straightedge to identify warping or distortion that can cause large bubbles. If necessary, flip your kiln shelf over and fire on the opposite side or replace the shelf altogether.
Eliminate the small bubbles described in Step 1 by using the following techniques that reduce the amount of air trapped by pieces of glass or increasing the time available for bubbles to escape. Cut smaller pieces of glass, prior to fusing, to reduce the likelihood that the melting glass will trap air. Similarly, cut smoother pieces of glass, rather than textured ones, to reduce the chances of air getting trapped between pieces of glass. Fire your glass on fiber paper, rather than kiln wash, to allow more air to escape. Support the edges of your glass with small glass beads in the same color as the glass, to give air more room to escape. Slow down your fusing schedule between 1100 and 1300 degrees Fahrenheit; add a lengthy soak around 1250 degrees Fahrenheit, giving your bubbles time to escape.