So it seems like every time I use royal command, after the creeps start moving again they get a damage buff and mow through my formation. I will be fighting a boss and kill all his minions. He will slowly beat down my tank and I will use the ability to freeze the boss allowing my tank to heal. But when the boss starts attacking again, it just goes through my tank in a couple seconds despite the fact that it took a significant amount of time to knock down the health of my tank the first time around. Does anyone know whats going on?

Ever notice that red aura building up around a boss? That is basically this game's version of the game mechanic called an "enrage timer".

(At least that's the name I've heard for the concept in The Old Republic, the only MMO I've cared to get into. There's a hidden timer on the large group bosses which will drastically buff the boss's damage output after a certain amount of time. Typically resulting in a wipe unless you were already really close to finishing it.)

Other clicker / idle games might just flat out put a 30 second timer on the screen and automatically kick you from a boss fight if you fail to finish it within that time. (Of course those games don't actually have enemies capable of fighting back. Everything is effectively just a fancy punching bag.) The approach in Crusaders is instead to slowly ramp up the damage output of the boss so that it will eventually overwhelm your defenses if it takes you too long.

Edit: I noticed just before a reset (which I've been doing on the mobile version lately) where I pushed through one last boss before resetting that the mobile version doesn't seem to have the red aura I mentioned. Instead it seems to visualize this effect with sparks swirling up from around the boss's feet.