Tommy Wright’s side named new signing Daniel Armstrong among the substitutes for the season opener at K-Park Academy after bringing the winger in from fellow Championship side Raith Rovers this summer.
However a suspension in the league cup competition carrying over from his days with the Fife side was still applicable and Killie played the 23-year-old for the closing 18 minutes of the game when he should have been ineligible.
SPFL chiefs are now investigating the rules breach and have summoned the Ayrshire club to a Hampden disciplinary meeting on Thursday.
It read: “The club would like to apologise to our supporters, East Kilbride and to the footballing authorities for this inadvertent breach of the rules. A hearing with the SPFL has been scheduled for Thursday, July 15 where the club will make representation.
“Until then, we will make no further comment.”
It adds to Killie’s recent woes in the competition which they won under Kenny Shiels in 2012.
Last season the club was forced to forfeit their opening game with Falkirk, handing the Bairns a 3-0 win, after a covid outbreak at Rugby Park. The enforced defeat contributed to Alex Dyer’s team being eliminated in the group stage.
Three games at the weekend, involving Ross County, Dumbarton and Morton went a similar way with each team forced to concede a 3-0 walkover defeat.
Kilmarnock’s next match is at Clyde on Saturday.