When a horse seems to react excessively to a hand touching these areas, the problem can be strictly behavioral or can relate to any of a variety of underlying conditions.
Assess the horse's general health using the Whole Horse Exam (WHE), paying particular attention to the area of concern. Look for any abnormality like swelling, heat or skin abnormalities. Then, try to determine whether this is a behavioral issue or physical problem resulting in pain or discomfort by performing the two skills Modify Behavior, Desensitize to Touch.
If you have any doubt, or notice any other signs of illness or disease, contact your vet with your findings and concerns.
Your vet evaluates general health and repeats the stimulus and observes the behavior. Through this assessment, they should be able to differentiate physical from training issues.
Can you detect swelling or heat in the area?
Has the horse been showing signs of abdominal pain (colic)?