Should a periodontal probing hurt? Was it going too deep?

It felt like a pin sticking me. The prior visit I had a deep pocket (6) in a tooth. (I've had deep cleaning already.) I had improved the tooth much since that time and had changed flosses and had no bleeding on flossing or brushing in six months. The gum around the tooth also looks nice and pink. The painful probing was a new hygienist and after looking at the prior records, I think she expected the pocket to be deeper. Once again, should periodontal probing the pocket hurt? Can they go too deep? Could this cause damage by going too deep? Thanks.