Here's the language of the new rule for this season:
"9.1a
To require that to be in the windup position, the pitcher shall stand with:
a) His chest and shoulders generally facing the batter,
b) His pivot foot touching on or in front of the pitcher's plate and
<b> c) The free foot touching or behind the plane of the front edge of the pitcher’s plate.</b>
Rationale
To clarify the windup pitching position for umpires to properly apply applicable pitching rules and to further distinguish the windup position from the set position. (A diagram will be included in the rules book.)"
Evidently Self had his front foot in front of his pivot foot, which is a no-no for some reason. He was warned, and then the ump called an illegal pitch, which turned a 1-2 count into a 2-1 count. After some discussion, Self pitched out of the stretch the rest of his appearance.
It's a quirky thing and I don't know why it hasn't been ironed out before the 20th game of the season- but apparently no one has called Self on it until now.