Hmm. This is a bit complicated, I’m afraid, and I think the biggest question I have before answering this is whether or not your croagunk displays this aggressive behavior towards just your father or towards bullying or abusive behavior in general.
If the former, then what you’re seeing may actually be anger towards her own treatment. She may see the fact that she now belongs to you instead of your father as protection; she doesn’t have to face your father’s treatment if she acts out towards him, as you’ll pull her away before your father can punish her.
On the other hand, if it’s the latter and it’s a general response, then it may be tied into her bullying tendencies. There is always a reason why anyone—human or pokémon—treat others the way they do. The simplest and most common explanation, though, is that bullies have faced abuse of some sort themselves from a very young age. In many cases, bullies seek out weaker targets than themselves in order to either release their own frustrations or treat them terribly out of the idea that this is just normal interaction. It’s possible, given that you’re not entirely sure what your croagunk’s past was like, that she was on the receiving end of a heavy amount of abuse, perhaps since she was a hatchling.
However, bullying can be corrected. It starts with establishing that your croagunk’s in a safe environment. Provide for her and give her affection whenever you can until she understands that you’re there for her and will care for her. Of course, pay attention to her body language at all times and give her space if it seems like she’s distressed or about to become aggressive. This will also help her understand that you know her boundaries, which will make it easier to reason with her and win her over.
Once she begins to feel safe, you can work on training the more aggressive behaviors out of her. Pokémon are far more malleable in this regard. (That is to say, don’t attempt to shower a human with affection if they’re abusive towards you, and certainly don’t try to “fix” a human’s aggressive behavior. If you find yourself in an abusive relationship, please use whatever resources you have to get out of it.)
With pokémon, meanwhile, respond well to simple Pavlovian training. That is, when your croagunk shows good behavior you wish to reinforce, reward her. When she shows aggressive behavior, don’t use aggression yourself to correct it; rather, tell her that this behavior is not proper. When she realizes she can be rewarded for certain types of behavior, she will begin to learn that following similar behaviors will result in more rewards. You can even use this technique to teach your croagunk the difference between aggressive and peaceful resolutions. Whenever she does something gently, reward her. Whenever she interacts with one of your pokémon in a positive manner, reward her then too. If she doesn’t, then simply scold her verbally (with a calm but firm tone).
Additionally, yes, some of her bullying behavior is dominance-based, as of course, your croagunk likely sees the rest of your team as weaker and therefore acceptable targets. You may need to establish her order in your “pack” as it were through establishing that she isn’t the dominant pokémon. For example, dominant pokémon in a wild herd are fed first, so by feeding your croagunk slightly behind the other members of your team (that is, giving your other pokémon their bowls first and then giving your croagunk hers), this will help her understand that, if anything, you are the herd (or army, in her case) leader. This will also help you train that aggressive behavior out of her, as it will also establish that she needs to follow you to be rewarded and to move within her team.
Finally, you may need to reintroduce your croagunk to the rest of your pokémon after her behavior reaches an acceptable level. This doesn’t mean separate her from the others as you’re training her (in fact, she should be allowed to freely interact, although yes, you should separate her from the others if she’s bullying them again); rather, it means gradually introducing her to individual members of her team and helping her establish healthy relationships with each member. In other words, serve as a mediator between your croagunk and your other pokémon. Have them work together on tasks. Encourage your croagunk to interact with your team in a positive manner.
Best of luck!