Bleh, rewind bugs.
You'll get a faster response (and more people digging into your log) on the Discord server in #mod corner: https://discordapp.com/invite/aQrXEse

Brief overview: The game stores mission info in the form of an RNG seed and a history of the actions you take. When you use a rewind, it basically retraces your steps from the beginning of the mission until the new current moment. Incidentally, the same thing happens when you load a save after exiting during a mission! If you exit the game, go into the game files and change them (or update mods!) and reload the game, you will get a different result than what you actually saved. However, this can also happen when actions taken in the mission alter the internal logic of variables in the mission. This is usually pretty rare, but can happen as an oversight. So one set of variables applies when you initially play the mission, but when it's "replayed" for a rewind or a load, the variables have been changed.

Unfortunately, this makes these bugs really annoying to track down without the user getting half into modding themselves. I'd suggest trying to find if there's a pattern, e.g. try starting a campaign with the same agents but different programs, or vice versa, and see if you still have the problem.

And as suggested, join us on Discord. : D

I see. I didn't realize rewinding was that prone to oddities like this. I'll try to get some more details if this happens again, and I'll keep the Discord in mind for the future. Thanks for the reply.