For the difficulty, I think most people complain about the nuns' healing. It has been nerfed significantly for the next version.
Overall, as more stages get released the resource stages will get more spread out, thus making it possible to reduce their difficulty. As it currently is, I had to somehow make the "endgame" of the current version somewhat challenging, thus the power of enemies.
Saving is done every 5 seconds in the background. It also saves upon game close. So when a crash happens at the perfect time, aka when the game was saving, it corrupts the files. I have fixed this problem for the next version so it will be better for sure.