If you're otherwise happy with the container, I would try to exchange it. Now that you know what a potential pin prick hole looks like, hopefully you could inspect the replacement for one before walking out of the store.

Water does not need to be kept in an airtight container during storage. Clean water, stored in a clean container, kept out of sunlight, should not grow anything, regardless of whether the water is sealed or not. Unless you're getting a strong plastic taste (which probably would go away with a number of water changes...or not), I think rotating every three months is unnecessarily short. You could easily go six months or even a year between changes.

By the way, I wouldn't call the vent hole a defect. If water is coming out out of the vent, my opinion is that you overfilled the container beyond what the manufacturer intended.

But good for you for making the effort towards preparedness!