Recent endoscope showed I had GERD and bile reflux. Hida scan and ultrasound were negative for gallbladder issues. Why do I have bile in stomach?

Some bile is normal. The stomach's outflow end is not a one way valve. It will let some bile into the stomach. The acid environment of the stomach takes care of it. When bile makes it all the way to the upper end of the stomach and backwashes into the esophagus, then it is bile reflux. This will cause irritation to the lining of the esophagus and there are no pre-made defenses to it, like in the stomach.
Bile reflux. Bile reflux is a diagnosis not made on endoscopy, but it can be suspected. The diagnosis is made on ph studies using a specialized capsule. It is normal to have a small amount of bile in the stomach. A hida scan is worthless for this, and the gallbladder has little to do with this. It relates back to the valve on the lower part of the esophagus. If weak, you will regurgitate both acid and bile.
Bile reflux. Bile in stomach is usually due to bile from duodenum going back into stomach, duodenogastric reflux. This can be due to duodenal dysmotility. Bowel obstruction can produce a similar problem but usually results in vomiting bile.Bile in stomach can sometimes cause gastritis.Patients with cholecystectomy sometimes have this problem. Duodenogastric reflux often can be diagnosed on hida scan.