A 12-ounce glass bottle is designed to hold 12 fluid ounces, which are a measure of volume. Fluid ounces and standard ounces are not equivalent units, as standard ounces are a measure of weight.
Ounces, in the case of a 12-ounce bottle, indicate how much empty volume is available inside the glass bottle, rather than the bottle's weight or the weight of any objects that may fill up the bottle. The volume inside a 12-ounce bottle is equivalent to 1.5 cups of fluid.
Water is the only common beverage or ingredient where units of fluid and standard units are interchangeable: the amount of water in a 12-ounce glass bottle weighs 12 standard ounces. For other ingredients, the two units vary, sometimes drastically. For example, 8 fluid ounces of flour weighs 4 standard ounces.