Can I fix my bad training?

So I've had my pup for about 3 weeks now and she's my girlfriend and I's first dog. We got her a crate about a week in and we've been using it to help potty train her to only potty outside (which seems to be working well). Within the past week I've been learning more and more that positive reinforcement is the only real way to go with dog training and I just now read that crates should NEVER be used as a form of punishment or "timeout."

Here's where I've messed up. Whenever my pup did something wrong or had prolonged episodes of misbehavior, I'd use the crate as a "timeout" zone and/or scolded her while she was in there. I've also done what a guide said never to do which was "NEVER force your dog into their crate."

I'm worried that my pup has formed a negative association with her crate and doesn't think of it as a safe place (understandably) and it's further backed up by the fact that she never goes in there on her own accord to sleep or rest.

Have I permanently built up a negative association of the crate for my pup? Can I still build a positive one from here?

Any help and advice would be greatly appreciated! Sorry for the cringe you might be feeling towards our amateur training. Thanks in advance!