Thanks for the feedback! There is no way to save ingame, unfortunately, its just in-between missions and specific checkpoints. It is a little concerning that it crashed, I've never had that happen and I alt tab out of the game regularly. Can you tell me what OS you are using and how the crash happened exactly?
The levels are meant to be more like a strategy game where its balanced around the units you start with so carrying resources/units over would break the balance. It's mostly the introductory stages where you only have one or a few units but I think that gives people the wrong expectations. I will think of a way to explain that better.