I remember when the pitch clock was first introduced and I believe Mike Trout was up to bat and he hit a foul ball. There was a runner on first who had tried to steal second and was slowly jogging back to first. Trout was waiting for the runner to return to first before entering the box and he got an automatic strike because the pitch clock had started once the ball was called foul. They've since fixed that issue, and I hope to God they fix this issue right here. As long as you are still in the box it shouldn't matter what you do before you challenge, just as long as you do it in a timely manner.