The Whites were incensed by a number of referee Darren England's decisions, including the awarding of a goal-kick after a wonderful save by Lions keeper Bartosz Bialkowski.
Millwall were also given a penalty seconds after Leeds felt the ball went out of play.
Writing in his programme notes for today's game against Wigan Athletic, chief executive Angus Kinnear revealed the club's concerns over the standard of refereeing in the Championship have only been exacerbated following the midweek clash.
"The only negative from the match was that the standard of EFL officiating was once again brought into question," he said.
"While most of our feedback to the match official assessors this season has been around interpretation of the rules, some of the decisions against Millwall forced us to add 'simply not paying attention' to our list of concerns.
"I am confident that Leeds United provide the most comprehensive post-match feedback of any Championship club. Our report on the Millwall game highlighted 17 separate decisions that we felt were worthy of review and, to the credit of the assessors, they will review the video of each decision and provide a perspective in return."
Kinnear says the club don't buy into conspiracy theories but they are aggrieved at how many points they believe have been lost as a result of poor officiating.
"Hopefully this endeavour can lead to an improvement over time, however in the short term the fact that erroneous decisions have conservatively cost the club over 10 points this season is cause for significant concern," he said.
"As we do not believe there is any anti-Leeds conspiracy or agenda, we can only conclude that EFL referees have challenges with handling the pressure of higher profile occasions."
The FA have charged Leeds director of football Victor Orta and head of communications James Mooney over their conduct during incidents at half-time in the tunnel on Tuesday.
Both will accept the charges.