the possible reasons:
1) Hygienist was too aggressive and not careful when cleaning the gums around your teeth causing trauma. (Not likely if the same hygienist you always see).
2) Previous cleanings were not performed well, leaving buildup below the gum line, and the hygienist had to really get in there and clean.
3) The cleanings in the past you had were regular above the gum prophylactic cleanings, and the most recent cleaning you had is "deep scaling" or scaling and root planing to treat periodontal disease.
4) Using a new toothpaste or mouthwash since the cleaning. (Possible allergy).
5) Bacterial infection. If a more thorough cleaning up you teeth was needed, sometimes bacteria can find their way inside your gums at the junction of where your gums meet your teeth.
5) My recommendation would be to take 400 mg ibuprofen every 6 hours for a couple of days (If you do not have an allergy to it and are not taking any other medicines) and rinse with the original (antiseptic) or all naturals Listerine mouthwash three times a day for a minute each time.
6) If things do not get better, then you should see your dentist, other things that can cause generalized swelling and soreness of the gums can include lack of certain vitamins as well as autoimmune diseases.
It would be highly unlikely for it to be autoimmune related but if you have no improvement you should consult with your dentist.