I played in Browser (Firefox), Steady state, I started switching machines off since I was running out of energy. Didn't seem to influence the loss. I will trying to replicate and see how long it takes between the drops and if I see any correlations to actions taken in game.
Edit: Played about an hour, researched the rotator and produced the *400 Quadron when the first 0.01 loss appeared. (see screenshot)
Edit2: Left the game running over night and didn't get another 0.01 loss. So it must be induced by some action.