Cleveland GM Mark Shaprio thought he had a good case but ...
In a memo from the league office explaining [MLB president and chief operating officer Bob] DuPuy's decision, Rule 9.01(c) is cited.
"The Official Baseball Rules do not address when the umpires can make such a correction in those circumstances," the memo read. "When the rules do not address a situation, Official Baseball Rule 9.01(c) gives them the discretion to rule on any point not otherwise covered by the Rules."
Shapiro jokingly referred to the rule as an "escape hatch."
You can get a rehash of the events in question by reading the linked article.