I recall having the same experience, but wasn't careful to track details, so I don't find a way to replicate this.
Water Pipes
as a free building given by Department of Water requires the following condition to be auto built:
- Fresh water.
- Metal wares are NOT required, since they are defined with <PrereqBonuses>, not with a <ConstructCondition> tag, which the auto-build process tests against.
Note that you still need the metal wares (copper, lead, iron, steel) besides fresh water to build Water Pipes in one city in the absence of the Department of Water.
Nothing I can help here. Next time when this occurs, try a recalculation. It should bring the free buildings including free Water Pipes back.