"Bubbles" are air or gas filled cavities within the glass. The image to the left is a close-up of a bottle with bubbles in atypically high quantity for illustrative purposes. Bubbles are caused by an assortment of irregularities in the production process including a glass pot or tank that was too hot or not full enough, glass cut-off or shearing irregularities, and various gob feeder problems. In the glass making industry, small bubbles were referred to as "seeds" and larger bubbles as "blisters" . Similar to the color question above, the presence of bubbles in the glass can help some in pinning down the date of a machine bottle, but must be used in conjunction with other features to more confidently narrow down a date range as it is not conclusive by itself.
Some pepole - believe that "the number and size of bubbles has absolutely no connection with the age of the glass." This appears quite true of mouth-blown bottles, though empirical evidence suggests some dating trends with regards to machine-made bottles. More specifically, there appears to have been an increase in the homogeneity and uniformity of glass as the technological advances of the machine era proceeded. However, this feature is still a tenuous one since there are many early machine-made bottles with few or no bubbles. Conversely, machine-made bottles after the 1920s which have numerous and/or large bubbles exist but are rare . See the Bottle Body Characteristics & Mold Seams for more information on bubbles.
If one takes a look at glass bottles found in supermarkets today they would be hard pressed to find even one bubble in all the bottles looked at combined as technology has all but eradicated this flaw in glassmaking.