Just to be sure...
When you subbed in the P to pinch run, for the injured player, his position should have shown as "PR". After all that is all you did was insert a pinch-runner, not a pitcher. After the inning played out you would need to designate him as the pitcher by changing the "PR" to "P".
Did you change "PR" to "P" to actually make him the pitcher for the next inning?
If you did all of that and had an illegal lineup then you have an issue.
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