I only play with the normal Crisis, no x2 or x3 or anythign silly so they're very manageable on a small galaxy (though maybe if it's your first time running into them, that may be uch harder especially if you still use Sapient AI computer on your ships) , of course out of their initial spawn in which they have a couple of super strong fleet tearing apart the surrounding systems without any possible counter.
But once they are done with their initial attack, they will expand a bit and to do so they will stretch their fleets out.
And starting from then you can then destroy those weaker assault fleets one by one (even more easier after the Cybrex helpers are spawning, as after their spawn all the Cybrex super strong fleets are at the same location and will then carve a path for you until their fleets will start to separate).
As you should have researched enough to meet their firepower anyways (as Stellaris like in all 4X research is super important to get ahead of everything), and by the time you reach their various nests (the "Sterilization Hubs") you can focus all your ships on one to take out the super strong defender of each hub world without that much problem, especially if you have arc emitters weapons that absolutely murder Contingency ships.
After taking out a Sterilization Hub, all you have to do is heal/replace losses then go focus all your ships to the next nest, repeat until all the nests are dead and the Contingency is finally dead after you destroy their homewolrd.
But it also shows something that is still very bad in Stellaris : orbital bombardment.
Because to take out a Sterilization Hub, there is only one way : orbital bombardment, and in Stellaris orbital bombing simply takes forever to achieve anything, and even worse, regardless of sending a couple of ships or a thousand to bomb a planet from orbit it will take the same ridiculously long amount of time.
In fact i think it took me more time to wait for a Sterilization Hub to be fully bombed (at least it is considered dead at "only" 50% of devastation, but it takes insane amount of time to reach that number) than to fight back and capture systems during the whole crisis.
This is made worse by the terribly bad AI that does not even try to send his remnant ship to come to the rescue of its own currently bombed world, it's basically a very boring wait unfortunately totally uneventfull.