Ultrasonography is one of the best imaging options that doctors are able to use in order to get a good overview of what condition a patient may be dealing with. It is noninvasive, relatively cheap and extremely convenient for doctors to use so treatment can be initiated as quickly as possible.
Most of the time, the only complaints that patients will have when they go for an ultrasound scan is the unpleasantness of the gel that is necessary so the probe can get a good picture of the area of concern. It does not hurt, it is just cold so patients will be able to quickly acclimatize within a few minutes. In some cases, however, patients may experience patient with the US test which could suggest some underlying pathology.
One of the most common reasons that patients will have abdominal pain after an ultrasound examination would be due to inflammation of the pancreas. The pancreas is one of the key organs that physicians are able to visual with the US machine and any type of inflammation leads to a condition called pancreatitis. This is an extremely common problem and patients who drink too much alcohol, experienced some type of recent trauma or have any type of pancreatic stones are at risk for this condition. Any type of pressure will be an obvious discomfort for the patients so it is something that could be responsible for your pain.
Another possibility would inflammation of another important organ that we visualize under US. This would be your liver. This is an organ that can also be inflamed if you had a recent hepatitis infection and due to its deep anatomical location, it is something that a doctor may have to use a lot of pressure in order to visualize.
Pain is something that is quite subjective, just like the skills of the person performing on the ultrasound machine. Beginners who do not have a lot of experience with the machine may be unaware of the sensitivity of the probe and may exert too much force thinking the best way to visualize internal organs is by getting the probe as close to the organ as possible. This can be extremely unpleasant for the patient but it should not be life-threatening by any stretch of the imagination.
Another possible reason why the abdominal US may hurt is due to the consistency of the superficial abdominal tissue. Patients who have excessive abdominal fat pose a challenge for abdominal US examination because the layer of adipose tissue between the probe and the internal organs can make it difficult for physicians to locate the internal organs. Doctors will have to apply a little extra force in order to try to get the probe as close to the internal organs as possible with can manifest as unpleasant pain for the patient.
Patients also apprehensive about this procedure are also at risk of having discomfort during the procedure. When abdominal muscles are tense, it is more likely that they can be accidentally injured when a probe is passed over their body. Patients should try their best to relax and may benefit from bending their knees while lying on the examination table in order to relax their abdominal muscles. 
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