Puppy cries when I’m around and she’s in her pen alone but settles quickly when we go out?

Hi guys! I got a cockapoo pup 2 weeks ago, she’s 11/12 weeks old. I’ve had a dog before when I was a teenager and my husband hasn’t.

We naively thought this would be easier than it is, we knew it would be hard but not this hard!

She cries when I’m around the house and she’s in her pen alone. When we leave for work she cries of course but settles down relatively quickly so I’m not sure if it’s separation anxiety or not? I work shifts and my husband wfh 2 days a week so she’s not always alone for hours and hours. She sometimes will pee and poo when we go out and I try not to be annoyed because she probably just needed to go but sometimes when we go upstairs to get ready she will just poo because you leave (or at least that’s how it feels) 😅

She loves her crate and she goes in there by herself when she’s tired or to calm down. We had a pen that we opened up but I now think I’m going to close it up again into an actual pen for her to use.

But please, how long till it gets better?! We’ve had a tough year and thought it would bring some happiness into our lives and it has but also a world of stress and tiredness and frustration. She’s just a baby and we know that but it’s hard!