Jeff, I came across the following information through Google.

Are you familiar with the Goldsborough brothers? Major William Goldsborough of the Confederate 2nd Maryland Infantry captured his brother, Charles, who was a surgeon in the Union 5th Maryland Infantry.

The following link tells their story:

http://perspectives.jhu.edu/2011/05/national-strife-pits-brother-against-brother/

Also the following passage from the Confederate Military History, volume 2, mentions that William captured his own brother.

http://www.civilwarhome.com/marylandcmh9.htm