My 12week old is the same. If she's tired and I put her in the crate she is fine, but if I put her in there during the day, or even at night before she thinks shes ready for sleep, she goes nuts. Crying, barking, scratching, clawing, chewing her bedding and throwing herself at the door of the crate!
Have you done any crate training with her, or just put her in the crate and expect her to be ok with it? With Max I often put her in there for short periods (literally a few minutes) and let her out/reward her the instant she stops crying and settles down. The length and severity of her distress is slloooowwwwly lessening (very slowly!) but we've only been at it for a few weeks so I expect with extended work she will eventually settle down and learn to like the crate a bit more.