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Cats are physically pretty robust and it's unlikely you'll have hurt her by pushing her into the carrier without knowing about it; she would have yelped or hissed etc.
More than likely that she's misjudged a jump exploring her new home or something.
If she's not eating and struggling with movement, though, I'd get her to the vets ASAP. Cats can mask issues and deteriorate quickly if it's something serious. I'm sure it's nothing but it's always better to be safe than sorry...
Soul
Thanks for the advice. I just pinned her to the ground and then put the towel over her and wrapped it tight. I think I may have hurt her the first time when I didn't use a towel and just tried to push her in. She obviously just clawed the sides of the carrier and used all her might to stop me pushing her all the way, so I may have hurt her then. She never made a sound though.
I've never tried lifting her by the scuff, does it stop them from wriggling around / claws of death?
Gave a vet a call and she reckoned to give it a few days to see if she improves and if not to bring her in. She can put weight on the leg though so I'm hoping its just a sprain or something.
Arrgghh. My first experience of being responsible for another create and I've screwed up within days.