Worried that we’ve spoiled our puppy; want to fix it before too late

Background: My wife and I brought home a 10 week old female maltipoo in August. She’s now 17 weeks and doing great. Has all her shots and responding well to most training. She’s very comfortable with us and in general is a sweet, mild tempered puppy.

The issue: I think she’s becoming too much of a Velcro dog… and my wife and I haven’t helped the situation. I’m a first time dog owner and I’m completely smitten with this dog. I just want to hug and squeeze her and give her kisses (which I do… a lot). She follows us around the house and doesn’t want to leave our side. It’s very endearing, but I know we need to foster more independence in her. It’s gotten to a point where I’ll be sitting on the couch with her and if I get up for a glass of water or leave the room for any reason, she hops down and follows me.

For the first month or so, she was doing pretty well sleeping through the night. We have a crate setup within a bigger playpen, and since we’re in an apartment, we would put her potty pad in there too. We’d put her to bed around 8-9pm and she would wake up around 5am. Well, eventually it became 4:30 then 4:00 then 3:00. After waking up and going potty, she didn’t want to go back to sleep. Our solution was to bring her up on the couch and one of us would sleep with her for another 3-4 hours. This was working well, but I believe is the source of the problem.

Now when we put her to bed, she either doesn’t sleep or wakes up in an hour or two and barks and barks, refusing to go to sleep. We live in a basement apartment and don’t want the noise out of respect for our neighbours. She also doesn’t like being crated anymore. For the first six weeks or so, she was doing well in her crate up to a few hours allowing me to go grocery shopping or whatever, but now she’s immediately clawing at the door and crying/barking. I was doing a good job of enforcing naps and she was taking to it for the most part. She’s showing some pretty distressing signs when we leave her in her crate and doesn’t like being left alone in her pen even when there are plenty of toys and treats.

Solution: I believe the solution is we need to be firm with her and leave her in the crate. I think we need to start crate training from scratch and reintroduce her to it. To be fair, we didn’t do a lot of formal crate training. Just fed her meals and treats in there. She wouldn’t often go in on her own, but didn’t object much to us putting her inside.

It’s hard as a first time dog owner trying to sift through all the great information online. When she’s whining, crying and clawing for 10-20 mins straight it’s hard to ignore her. I gave her with a Kong stuffed with food the last time I left her in the crate and she completely ignored it—she pulled her crate cover through the bars and dug up her crate mattress pad. It’s also hard to tell how much of this is puppy behaviour/improper crate training on our end vs potential separation anxiety rearing its head. She’s only 17 weeks so I think any bad habits can be unlearned. Just looking for guidance and advice here. Thanks everyone.