As far as I know, the Botnet does in fact do reclamation damage.
From the first line of its description:
"Reclaims enemy ships it kills (reclaimed ships have health = full damage inflicted by reclamator). Reclaimed ships come back as Zombie Bots, which cannot be controlled but which will attack enemy ships mercilessly until they die."
Now, if you mean you are reclaiming ships into your control, not as zombie bots, then I'm not sure.
Did you grab a leech starship by accident when selecting your fleet earlier?
Also, did you have ships run away earlier? It is possible they were survivors of a previous attack on your whipping boy.
I'm not sure what the conditions for clearing reclamation damage is, I've had ships take damage from parasites and not lose them to AI control until 20 minutes later when a different wave of ships actually killed them.
D.