Since neither one of us was there, we will never know.
Stephen was a Roman, and the son of John, a priest. He had been consecrated Bishop of Anagni, possibly against his will, by Formosus, and became pope about May, 896. Whether induced by evil passion or perhaps, more probably, compelled by the Emperor Lambert and his mother Ageltruda, he caused the body of Formosus to be exhumed, and in January, 897, to be placed before an unwilling synod of the Roman clergy. A deacon was appointed to answer for the deceased pontiff, who was condemned for performing the functions of a bishop when he had been deposed and for passing from the See of Porto to that of Rome. source.
Regardless of the circumstances, he never erred in doctrines of faith or morals.
What was the substance of the stated disagreement between Pope Stephen and Pope Formosus if not over doctrine?
Either Pope Formosus was in error for performing the functions of a bishop, or Pope Stephen was in error for condemning him for it.
It seems to me that it is impossible to have both be correct over the doctrine they ‘argued’ over.