Purely speculating, but a few factors come to mind. People want water bottles in a variety of sizes and shapes. The precise amount of water held may not be a primary consideration for all consumers. Design aspects such as grip ridges or handles can affect the volume of water that can be held. Maybe a design starts as a simple 32oz cylinder but after the volume is shaped, 3oz of volume has been removed. Now it's a 29oz bottle.

I imagine that the design of the bottle comes first in many cases. A bottle is made that can be used / stored / handled in a particular way and with whatever features. There may be an intent that it will hold "about" some amount of water, but it might not be worth tweaking the design further to get the volume to a specific number.