Placing waterfill under buildings (and vehicles, drones, etc) destroys the entity. This is fine and expected. The destroyed entity is not included in Kills/Losses statistics.
Is this a mod issue or base game?
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I'm using Klonan's Construction Drones mod. I noticed that several of my personal drones were missing. They have a habit of getting stuck in piping but also sometimes wander into range of a worm and get themselves killed. Looking on the production statistics screen, I can see the total number of bots produced and destroyed this game. Simple subtraction tells me how many I should have and need to find. Eventually I worked out that they had been "silently" destroyed

I did more testing, deliberately placing waterfill under buildings and routes where drones where travelling. Buildings and drones destroyed this way aren't included in the kill stats.
Thanks!