Inspect your wine bottle for small bubbles called "seeds." Seeds are manufacturing defects, and if they are present in your unfired bottle, nothing can get rid of them. Start with a bottle without defects.
Check your kiln shelves with a straight edge to make sure they are level. If the shelf is warped, turn it over and check the other side. If still not level, replace the shelf.
Place your bottle on thin fiber paper instead of using kiln wash. Fiber paper lets more air escape from the glass, and gasses released from kiln wash may create bubbles that grow and eventually pop, leaving a hole behind.
Slow down your firing schedule to 1,100-1,300 degrees Fahrenheit to keep the glass from melting too quickly and trapping air. You also can add a "soak" at about 1,250 degrees Fahrenheit to give the bubbles more time to escape. Soaking is maintaining the kiln at one specific temperature for a period of time. Your firing schedule will depend on your kiln, and it may require some experimentation.