Yeah, the rogues were stealing from you. If you popped them, they'd give it back and more, but I agree. The update I have planned for after this jam is over will make it so they can't drain any tiers that have been unlocked, or any fully unlocked buildings. And the rogues will start dropping a bit more to be noticeable, so the player can decide if it's worth keeping them around a bit longer. Hopefully those combined will address your issue there and make it feel more fair, while retaining the "they're going rogue, must pop them" feel.
Thanks for playing and the feedback!