Maybe she was hurt or disturbed by them at some point and you didn't
know it. (It's not always easy to avoid cutting the dermis, which is
very painful.) Or something else could've happened.

Try a different type of clippers. Either regular human toenail clippers
or the guillotine-type clipper sold in pet stores are used. Whichever
one you've been using, switch to the other and see how that works. HTH.

Don't let her see the clippers.
Cover her head with a towel when you do it.

When it comes to Matilda and nail clippers, tooth brushes and the crate for
trips to the vet, I get these ready well in advance and then catch her by
surprise and do what needs to be done. Works for me!

Try playing with her feet while she is very relaxed, preferably
asleep. Gently squeeze her paws to expose the claws, touch the claws,
massage her feet etc without the clippers being anywhere in evidence.
When she is ok with that re-introduce the clippers. Again do it when
she's sleeping, take it slowly and be prepared to do one foot per nap
for a while.

All the best with her.

Kate and Angus