I am pretty sure that nothing actually "caused" this to happen, but rather it was something there from the git-go.
Whenever an inflatable maker adheres a large, wide patch onto a tube, especially in areas where there are compound curves, it is impossible to not get a few small air pockets trapped underneath. This would happen whether the material was reinforced, or unreinforced gum rubber.
At the boat factories, most of the time there are larger bubbles in wear pads than what you are seeing here, and they are dealt with using a pin to release as much of the trapped air as possible. These pinholes or some degree of porosity in the gum rubber may account for the water in them.
We sell few NRS hypalon boats and don't have any pony in the race, but this can and does happen with bottom chafers on every brand of inflatable. Anything this small won't affect the performance of the tubes, though larger crinkles maybe could.
I don't know the details of NRS's serial numbers that well, but it looks like your tubes could be nine years old. If they are in good shape otherwise I would not worry about small bubbles at all. A better reason to apply liquid urethane to the bottom of any NRS hypalon boat would be to overcome their natural tendency to stick on rocks, something they tend to excel at.