I noticed that (at least since installing Noxys Waterfill) when I make a blueprint the naturally generated water of lakes is ending up in my blueprints if I choose tiles (for the purpose of detecting placed landfill). I can manually delete the water tiles from the blueprint, but it is a royal pain in the rear.

Is this a bug of the original game, or is it a bug of the Waterfill mod?

This is not a bug. Waterfill is meant to be blueprintable. It is very easy to remove all waterfill tiles from a blueprint though. A single rightclick on waterfill in the component list of a blueprint will clear all of that type. This shouldn't be a pain in the rear at all.

I think you misunderstood. I don't mean that the tiles "I place" end up in the blueprint. I mean water tiles "from the original lake" are ending up in the blueprint. I just did a couple blueprints, placed landfill on a lake and no waterfill at all, and water showed up on the blueprint - that had to be manually removed.

Only tiles "placed by the player" should end up in a blueprint, natural terrain should not... just like it happens with landfill vs naturally generated land. That is why I am calling it a bug.

I believe there is no distinction between water tiles placed by the player and water tiles naturally generated. Yes this does appear different from for instance landfill but if landfill generated naturally it would also show up in blueprints. This is not something I can change since the base game does it like this.