Some of the missions are designed to have inherently unfair map gen scripts, mostly because the AI is simply not capable of competing with a mildly experienced human player in a straight-up fight. The devs are planning to add in the option to play each campaign map on a fixed seed, though, which will help address some of the edge cases in map gen that you run into when you get further into the campaign and replay levels multiple times.
As far as that mission with the falcons attacking you from both sides, if that’s the one I’m thinking of, the best approach is to just bumrush the enemy with your entire starting force and just kill their mills before the first falcon wave shows up. The defenses in the current build of that KSR mission are about half of what they were on launch, so unless they gutted your starting forces (haven’t played it in months) it should be workable.
Generally, your army composition should have units that you can leave to their own devices (squirrels, lizards, skunks, falcons, etc.) and then a unit that needs to be micromanaged for maximum effect (toads, snakes, fox, badger, etc.). Between that mindset and the maps’ small size, I don’t really ever find a pressing need to split an army in nearly any situation, and that’s the case in a lot of modern RTS games. Bringing your entire force to bear against a divided army results in a disproportionate victory for you most of the time, which incentivizes having a death ball. T&T just makes that a necessity of the way the control scheme works.