The former Pompey defender wasn’t in the Dons’ match-day squad for the trip to Whaddon Road.
That’s despite reports that he travelled with the team, while there’s been no suggestion from the club that he’s injured.
Brown has featured 10 times for Wimbledon since his move from Fratton Park for an undisclosed fee at the end of the January transfer window.
However, he’s yet to experience a win for Mark Robinson’s side – who now sit in the relegation zone following their 3-1 loss to the Robins – prompting him to speak out about his new team’s form following their recent defeat at Plymouth.
He was expected to feature again against Cheltenham, but was nowhere to be seen as the team-sheet was released.
That led to many Dons fans questioning his absence – but, as yet, no explanation has been provided.
Taking to Twitter, @leewillett88 wrote: ‘Any word, please, on Lee Brown's absence today? It would be useful to know why he was missing. Thank you.’
@Davidscerri7 commented: ‘Lee Brown, not even on subs bench!’
@MLines05 said: ‘Why have we acted like Lee Brown doesn’t exist today?
Meanwhile, @AFCWTWEETS2 wrote: ‘Right those wondering I was in the ground at 2pm.
‘Lee Brown was walking around and I heard someone speak to him and he said he wasn’t injured.
‘Just dropped from the squad like Marsh was last week.’
When speaking out about the Plough Lane sides slide towards the relegation zone, Brown said his team-mates were ‘naive’ if they thought what they are currently producing is good enough to beat the drop.
Some have queried whether the left-back has paid the price for those comments.
Yet his words aren’t to dissimilar to those spoken by Robinson immediately after the defeat at Cheltenham, with the Dons now 19 league games without a win and in the bottom four for the first time this season.
‘We need a wake-up call,’ Robinson told the club’s official website.
‘We haven’t been in there (the relegation zone) all season – we have gone in there now.
‘The 19 league games (without a win) is just not acceptable – I am embarrassed by it myself and hurting.
‘This needs to change it. I will fundamentally keep working with the staff to give them everything, but they (the players) play the game when they go out there.
‘That’s not me throwing them under the bus, but they do play the game.
‘I ask them: “Do they feel as though they are getting enough from us to win games – tactically and in everything we do?’, and I get the same answers.
‘But when they cross that line, they have got to play the game.
‘For 80 minutes today (Saturday), I don’t think we were at our best, but we were fine and looked comfortable.
‘But we have walked off the pitch, and we have lost 3-1, and it ain’t good enough.’
Other results: Cambridge United 0-1 MK Dons, Charlton 2-0 Burton Albion, Crewe 0-1 Bolton, Fleetwood Town 0-0 Doncaster Rovers, Gillingham 0-0 Sheffield Wednesday, Lincoln 0-0 Sunderland, Oxford 1-1 Ipswich, Plymouth 4-0 Accrington, Rotherham 0-3 Shrewsbury, Wigan 4-1 Morecambe.