Problems with crate training (and possibly separation anxiety) in my 3 month old puppy

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So we recently got a puppy and she is a wonderful little girl, but we've been having some real problems with crate training and getting her being comfortable by herself. If anyone can spot things we're doing wrong or can make any suggestions, I would be incredibly grateful.

From day 2 or so she has been happy enough to sleep in the crate at night and will even take herself off to bed there, but during the day she hasn't shown any real desire to nap in the crate or be in it at all. We've put treats in there and tried to make it a comfortable safe space for her (her bed, blankets some toys and it's covered over the top and sides) but she shows no interest besides eating the treats and wandering back out. In fact, she often prefers plopping herself down on the floor closest to where we are and naps, and if we get up or walk away she follows and won't just nap by herself.

On occasions where we have tried to or needed to put her in the crate so we know she is safe when we go to take showers etc, she whines and howls like nothing else and will not calm down at all, even pulling the blankets over the crate into the crate through the bars and generally making a ruckus. Even when we know she has been properly toileted and desperately needs a nap, she somehow finds the energy for all this.

On a related note, if we do need to go upstairs during the day and close the stairgate behind us (she doesn't go upstairs is one of the rules in our house) she will often sit and whine/howl at the bottom of the stairs until we eventually come down. She won't go off and do her own thing with toys or anything, just sits and howls. I'm getting more worried that she just can't cope without one of us nearby, and this isn't good for her or us. I want her to be comfortable chilling on her own, and I fear that lockdown hasn't helped this at all.

I've been put in charge of training this dog as my parents are at work most days, and it's stressing my mum out especially that our pup won't settle in the crate as I will eventually go back to uni in a few months. I'm getting scared I've done something permanently wrong with crate training or my puppy not being able to be comfortable on her own, so please if anyone could point me in the right direction or tell me what to do/what not to do in these next few months I would be so grateful.

If you need any more information on what I'm doing I'm more than happy to provide it, I honestly just want the best for this dog and to help her settle in comfortably with us as her family for the rest of her life.

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