I understand you said his warm-up pitches are good but they are more than likely not at 100%. He may have an arm issue, especially after pitching the innings you mention.
Aside from an arm injury, I would take him on the side and cover up the plate so his primary focus is on the mitt. In college we always warmed up with the mitt about 6 inches off the plate inside/outside and worked our way in. Taught you to pitch to the mitt and not worry about the batter.