On May 31, 2014, the Federal Election Commission determined that it had overpaid Gary Johnson’s 2012 campaign $332,000 in primary season matching funds. See the 2014 document here.
On April 5, 2016, the FEC rejected the Johnson campaign’s argument that the 2014 decision was in error. See that conclusion here.
It is not uncommon for presidential candidates who receive primary season matching funds to later be found to have been overpaid. For example, in 1992, Lenora Fulani received $2,011,929.42 in primary season matching funds. In 1995 the FEC determined that she had been overpaid $612,557.32. Upon reconsideration, however, the FEC lowered the overpayment determination to $117,269.54.
Johnson received $632,017 in 2012 primary season matching funds. Thanks to Thomas Knapp for the link to the April 2016 document.