3 month old puppy growled at the vet.

hi! this might be a little long i apologize lol! i have a 3 month old great pyrenees/ pit mix. just for a little extra background information i have had him since he was born and bottle raised him. anyways, when we got to the vet the front desk lady took us back to the exam room. my dog was very excited when she was petting him, no issues at all. she left and i noticed him to seem pretty nervous and uncomfortable. i tried petting and talking in a calming tone. the vet eventually came in, said hi to me and gave him one little pet and automatically went to handling him. he was pretty tense and when she got to his genitals he let out a low deep growl. she backed away and told me to scratch behind his ears and try to distract him. he growled 2 more times after that but they weren’t as serious as the first time. when we were done and she actually started petting him he was happy, wagging his tail, and trying to play. she seemed a little nervous when he was trying to play, which is totally understandable but even after the growling she was even able to clip his declaw nails with no issue! i asked her if that was a little too much for a puppy this young. she told me “i will never punish a puppy growling but that was a little over the top”. i don’t wanna be blind or stupid to this behavior so that’s why i’m asking for advice on this. i feel as more so it was the environment, he was uncomfortable, and she didn’t do a good job taking a second to introduce herself and went straight to handling him. he’s never shown aggression towards dogs, kids, especially other people. he LOVES people. the only “bad” behavior i’ve seen from him is when he took a slice of pizza off the table and growled when i tried to take it but i just redirected him off of it with something higher value and he was fine after that.