If it happens again, you might send the last-autosave file :)
What I patched was a case where train was already forcefully braking (like changing a rail-signal to red through the circuit-network), the additional braking that the mod did, flipped the velocity to negative values. I capped it to zero. Hope it fixed it, but there may be another cause still. Anyway, I hope you enjoy the mod! Sorry I wasted 5 min of your time :)