Getting my stomach checked HURTS?!

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Discomfort maybe, pain is usually a no. I hope you told her about the pain. Also, did it hurt more after she released the pressure? If so, that's rebound pain and can be an indicator of something very serious. Like appendicitis. If you are still feeling pain, get checked, if not, well maybe your abdominal area was inflamed, or maybe she was a tad rough.

Actually a proper abdominal exam must be done while laying down or all the organs can't be palpitated.

To address your additional, what you describe isn't 'rebound' pain. You were probably a little tense during the exam. You sit in the waiting room wishing the exam was done with, your stomach knots and you tense up further. This causes inflammation of the gastric regions as more acids are produced. Then you tighten your muscles. So the palpitation caused pain. Relax I'm sure you're fine.
Take care.

Were you gassy or constipated at the time? Sometimes that will cause the type of pain you are talking about. Since the pain resolved and if it has not recurred since I would guess she was a little rougher this time. Tensing your muscles during the exam (and you may not even be aware you were doing it) could also make it more uncomfortable.

You should sit down if you want to check when your stomach hurts.