Can he seek custody becuase I brought my daughter to the hospital to get evaluated?

you did the right thing. maybe he did the wrong thing and doesn't want anyone to know, maybe not. your job is to find out why she is behaving why she is. get her to a counselor as soon as possible because the sooner you know the "why" you can start on the solution. so don't let him scare you, you are doing the right thing.