Wireless Capsule Endoscopy
Wireless capsule endoscopy cannot be used in patients with certain conditions. These include intestinal obstructions or strictures in the intestine or esophagus that might prevent the capsule passing through the digestive tract. Fistulas in the intestine can cause the capsule to become stuck in the abdomen and therefore contraindicate treatment. Swallowing abnormalities can cause the capsule to be aspirated and make the procedure dangerous. Patients who have pacemakers are also advised to avoid wireless capsule endoscopy out of a concern that the radio signal will interfere with the pacemaker.  
There is also the potential for complications with wireless capsule endoscopy. The most significant being capsule retention. In 0.75% of cases the capsule is not eliminated through normal peristalsis. When this occurs, there is a risk of obstruction and infection so the capsule must be surgically removed. 
More problematic are the technical limitations of current capsule endoscope technology. The frame rate and resolution are limited by the amount of power in the battery which is in turn limited by physical size constraints. The low frame rate means that a lesion might be missed if the capsule travels by without taking a picture. The low resolution makes it difficult to identify small lesions. Additionally, the field of view is limited by the CMOS size and the optical constraints of enclosing the device in a pill-shaped object. This means that problem areas might not be observed because they are behind the capsule.
Wireless capsule endoscopes are also limited because they lack the ability for active movement. They are carried passively through the digestive tract by peristalsis, just as food does. Regular endoscopes can be manipulated by the doctor to examine an anomalous area more closely or even to take biopsies or administer treatment.