Ion engine bug

When i was trying to get to the Luna using ion engine i discovered one bug.
Somewhy ion engine is producing negative thrust in timewarp,so instead of increasing my apoapsis i was decreasing it..
Steps to reproduce:
1. Build a rocket that can deliver something with ion engine, xenon batteries and/or solar panels into orbit
2. Launch that rocket.
3. Activate ion engine on orbit
4. Timewarp!
5. ???
6. Wtf? Why is it producing negative thrust?