Crate training, behavioral problems

Hey! I’m looking to see if some of you have advice.

I got my puppy Lily at 10 weeks. She’s now 15 weeks(almost 4 months). Since the day she got here, i put her in a play pen with her bed, pads and toys. She learned to potty outside and in the pad when needed very early on. I recently went to a training session, and the trainer told me to switch to a crate, so she would hold her pee and poop in. It’s had worked really well.

BUT, she will happily spend time in her crate after long excercise sessions during the afternoon. But in the mornings, after i take she eats and goes potty. I put her in her crate while i make breakfast and get ready, but she goes CRAZY. I mean she won’t stop biting, whining and digging her bed. I’m confused because she didn’t do this when she was younger, and didn’t do it a week ago when we switched to a crate. Should i leave her in there until she gets used to it? Why doesn’t she like it in the morning? I let her run and play plenty before i put her in. immediately i take her out she just sits in my feel and falls asleep. Why won’t she do it in the crate. She’s used to being there it’s nothing new.

Another thing, anyone have some behavioral changes i should expect this that’s she’s getting older? I’m finding her more stubborn, not coming when i call her and trying to escape, even when ive been training her and she behaved very well before.

If anyone replies, thanks for the help!