So the dog is considered by some to be still a puppy and maybe still learning/getting used to you if she's around three & if you aren't the first owner. It's a big possibility that she was abused by the prior owner (again, or spooked) which could be why she is reacting the way she is.
If she isn't all that used to your sister, that might be why she doesn't want to get into the cage ESPECIALLY if she already has issues going in. Please just be kind to her. From what I'm gathering, it seems like a genuine accident.
Slightly OT:
Is your guidance counselor the counselor at school? If this person is not a mental health professional and you mention to them that you thought your dad would abuse the dog, out of experience, they will most likely call Child Protective Services (CPS) (or what they also call DHS) which will mean visits to your house and interviews with everyone that lives there. If abuse is not an issue in your household and you feel safe, I advise against this.