Most ulcers that occur after gastric bypass are at the site where the gastric pouch is attached to the small bowel. Common causes include nonsteroidal anti-inflammatory medications, smoking, alcohol, or too large a pouch (large pouch -->lots of acid). Treatment includes medications such as omeprazole (Prilosec or Nexium) and stopping the predisposing conditions. Surgery is only done for bleeding, obstruction, perforation, or intractible pain.
Of course every operation has risk. The risk for this type of surgery is about the same as the risk of the gastric bypass itself.