I have one example. during the Cabin Creek Campaign of 1864 at the engagement of Flat Rock Creek, a brother was capture by his brother. I found a letter while researching for my book by a participate J. B. Stroud, who mentioned the capture of John Holden by his brother. I crossed matched the muster rolls for all the companies present at Flat rock creek and could not find that name. So I searched for like names and found a John Holland in the 2nd Kan. Cav. Company C. I also located Howard Holland who was in Howell's battery.
I hope this is what you are looking for. In that same engagement a father was also capture by his son.
curtis payne