When upgrading electric furnaces to multifunction furnaces from the mod krastorio, there is a low-ish chance (maybe one in 200 or so) of causing a desync. It happens most commonly when upgrading many furnaces at the same time using the upgrade planner and bots.
I don't think I would be able to find the bug by myself on this. Please send a bug report to the Factorio developers (in the forum), I would need their help in finding the desync bug. When you have done so, please post a link to the bug report thread here as well.
In version 0.18.2 and later the mod works in a very different way. Please try the latest version (0.18.3 just released today) and see if you can reproduce the problem.