The case of the Dole Foods class action payout has created headaches for share depositories and brokers. Short sellers arn’t too blame, or are the current bookeeping methods (although distributed ledgers would help). The problem is public courts inserting themselves into private contracts because of overbroad securities laws.
https://www.bloomberg.com/view/articles/2017-02-17/dole-food-had-too-many-shares