Some examples, as I said we would find them, we´re taking ... West Point class of 1857.
Instructors of Artillery (relevant years):
George H. Thomas (53-54)
James B. Fry (54)
Fitz-John Porter (54-55)
John Gibbon (54-57)
William J. Hardee (56-57)
Henry F. Clarke (56)
George L. Hartsuff (56-57)
Lots of instructors, with some commanding armies so it is pretty easy to fire on their commands. As for the cadets we have, being our perfect example, E. Porter Alexander. During the war he didn´t just have artillery in his command he was, for most of it, an artillerist - firing e.g. on Gibbon at Gettysburg, probably on Thomas around the early stages of Chattanooga and maybe on Hartsuff somewhere in the west. George A. Cunningham served as Confederate artillerist, too, and stood against Hartsuff in West Virginia.
We also have the interesting case of instructor versus instructor. Thomas on Hardee, and vice versa. Most likely Hartsuff has something in this, too. We also have artillery cadets opposing each other though I´m not sure if they exchanged fire, e.g. Alexander versus George A. Kensel around Petersburg and Appomattox or versus Charles H. Morgan at Fredericksburg. By the way, in this class we also have Richard K. Meade, who was present with Anderson at Sumter but joined the CSA afterwards.
But you already got my answer; I´m just using it as excuse to open the files again.