...no wonder!
You've spent 3 hoursish with your shoulder scrunched up holding onto a bottle. The nerve that runs through the muscle and down your arm is put under similar and unaccustomed strain - it doesn't like it.....
Don't stretch your arm, but improve the mobility of your thoracic spine a la roller and run tall - which is hard on long runs. Physio can help..
....and don't run holding a bottle 