You are using your crate to punish her, which goes against the whole idea of crate training.
Your puppies crate should be a safe place for her to retreat to.
You should stop doing this immediately.
To reverse the damage you have already done, I would recommend you start to feed her meals in the crate and leave treats in there for her to find so she can start to think of the crate as positive again.
Don't leave her in there for really long periods of time, try to make it only when she is sleeping for a while.
Before you put her to bed for the night, take her outside to the toilet and stay until she goes. Then praise her gently and put her in her crate.
At 3 months old, she should be able to hold her bladder overnight depending on what time you put her to bed and get her up.
Just in case, I would get up once in the night with her and take her to the toilet. Don't open her crate until she is quiet. If she doesn't seem interested in going, put her back in her crate.
Unfortunately, if she doesn't need the toilet, you will just have to ignore her until she quietens down.
She might quieten down quicker once you stop using it as a punishment.