vet behavior advice for puppy

Good Afternoon!

I'm a first-time dog owner, and I understand that there is room for me to grow. My puppy recently got sick (hookworms), and I brought him into the vet 3 times before they found what was wrong, telling me it was just normal puppy behavior, but I knew something was wrong (not sleeping well, fussy, whining, but stool was weirdly normal). At around 12 weeks, my puppy is still very nippy, but understandable due to teething. I freeze teething toys, provide enrichment, redirect, and train commands (sit, stay, paw, down) to shift his focus from nipping. At the vet, they examined him in the back, and she came back in and told me she was disappointed in my dog because he was aggressive. I noticed that he's been cranky ever since getting sick, but she told me that if I didn't sign him up for lessons with a private institute they're partnered with (250 per session), they wouldn't see him again. I understand his behavior was worrying, and I've already relayed the info back to his trainer so we can work it out when he feels better and curb this young (was told he growled at her).

I'm just feeling confused and lost, and would take any advice regarding getting him better used to being handled. He has gotten baths and nail trims from the groomer and me, and has never had an issue. My guess is that he was just stressed out already from being sick. He is already enrolled in obedience training, and adding another expensive institute doesn't seem ideal. He's a retriever mix, so he learns fast, but is extremely mouthy (as expected!) . Please let me know what I can do to improve his behavior moving forward!