Three Melbourne Victory players - Connor Pain, Giancarlo Galifuocco and Thomas Deng - Brisbane Roar pair Brandon Borrello and Jamie Maclaren, plus new Adelaide United signing Stefan Mauk and Sydney left-back Alex Gersbach - who appears on the brink of a transfer to Denmark - have been stuck in Doha after they were unable to book flights back to Australia.

Pain and Galifuocco arrive home on Monday morning, with Deng to return on Monday night.

The Olyroos were widely expected to qualify for the Rio 2016 Olympics but managed just a win against Vietnam, a draw against Jordan and a loss against the United Arab Emirates, leading to a group stage exit.

While all players are now expected to be back in Australia by Monday morning, Victory and Sydney are worst affected, given the pair clash on Tuesday in their traditional Australia Day match at Etihad Stadium.

Brisbane and Adelaide played on Friday night, less than a day after the Olyroos' last match - but the Central Coast Mariners were able to call upon goalkeeper Paul Izzo, who made it back in time for Saturday night's clash against the Western Sydney Wanderers, who themselves were unable to get Jashua Sotirio back in time for the match.

"The unexpected exit from the tournament at the group stage has caused major logistical headaches," an FFA spokesperson said. "Priority was given to returning A-League players to their clubs as quickly as possible, but there's been a shortage in availability of seats in what is peak holiday season.

"It's regrettable that some players have been delayed in getting home, but the National Teams Unit are doing everything they can to find flights."

The drama was amplified because every player selected flew to the Middle East on an individual booking, meaning that some players were able to return to Australia before others, regardless of their playing commitments back home. A pre-tournament camp in Dubai complicated the booking process.

Both the Sky Blues and Victory are expected to seek further clarification about how this situation was allowed to unfold, especially because the tournament fell outside a FIFA window.

If Gersbach does not play on Tuesday, the talented young left-back - tipped to break into the Socceroos' setup this year - might have played his last game for the Sky Blues.

It is understood that the club have reluctantly entered into transfer negotiations with Danish club Aarhus, former home of another Australian left-back, Shane Cansdell-Sherriff.

Gersbach's management team have been pushing for a European deal for the past year and the club has repeatedly tried to convince the youngster that his short-term future lies in the A-League.

However, while an overture from English Championship side Brentford was rebuffed in the pre-season, the club have become increasingly concerned they will lose the out-of-contract youngster for nothing in June.