Yes this can be an issue in a way, because it makes infinite water possible ANYWHERE, not just near a pond or river in a forest somewhere.

Basically water containers are able to have water taken out of them as if they were a water source, and that can make it easier to fill a bucket with water in your day to day scrap mechanic life. However, watering cans don't calculate the amount they take out of the container properly, and instead take one out per level of filling the can, so if you have a watering can that has 2 water in it, it takes out one water from the container, however it should take out 2 water from the container, because a watering can with 3 water in it can be turned into an empty watering can and 6 water, of which can be put into the water container.