Is it normal to get pimples or acne 6 weeks after a FUE hair transplant?

After a FUE operation pimples can come out. You did the best think consulting to your doctor. 

You can have pimples or folliculitis after surgery but you really can't expect a post on the Internet will solve your problem, can you?  The "feedback" that would be most valuable is contact your doctor and follow up with a face to face exam.  If it is an infection (even if it is rare) you cannot treat it unless you see your doctor.  Waiting for answers on the Internet may delay your treatment.

This is rare but when we see it, we have seen it last up to a year.  It is usually not an infection and follow up is important

There are many causes of donor area pimples after FUE. Without seeing the area, I can't give a definitive diagnosis.  The most likely cause by far, is "ingrown" hairs or folliculitis. It is not so much an infection but a type of what is best considered a "micro-infection" of the hair follicle caused by hairs trapped under the skin. Follow up closely with your surgeon and his or her team. Rarely the ingrown hairs need to be cut out or opened with a needle. Topical and oral antibiotics are helpful as are heat compresses and topical antibacterial agents (including benzoyl peroxide and triclosan containing shampoos). Sometimes this simply improves over time. 

If there is more than 2 pimples, then you may have folliculitis. This is an infection and you should see your doctor to find out if this is the problem because untreated it will have grave consequences.