Yeah, some of the missions absolutely do not want you to attack certain areas, if the areas are not specifically mission related, such as if you are supposed to be protecting civilians, or gathering minerals, they make the enemy bases crazy fortified, with almost no build time, and infinite resources. So, if you push in with a 200/200 army, you may think you are making headway, but they'll rebuild the base in a matter of seconds.

Just got to save constantly, and learn what areas are "forbidden". For instance, the level where you try to get the contract for Mira, don't walk up in the upper left and try to take on that main base until you've gotten her contract, or you'll get toasted by hero tanks and mass defenses. Kinda cool, but also, kinda lame. I haven't tried mass nuking such bases yet, though ^^