Football Federation Australia (FFA) opted to ban Perth from playing in the finals, but rather than consign the club to the bottom of the table it was decided Glory would be deemed to have finished seventh in the 10-team competition.
FFA said at the time it believed that course of action was "appropriate", but didn't elaborate on the reasoning.
Wanderers has had the A-League season from hell in terms of congestion, due to a combination of the final stages of last year's AFC Asian Champions League competition, the beginning of this year's ACL and a 25-day gap during which the club didn't any A-League games due to the Asian Cup break.
The break meant games had to be crowded even closer together on the schedule after that and at the worst stretch of it Wanderers had to play 11 games in 35 days.
The height of absurdity came when it played two A-League games within 48 hours.
It is a unique A-League season because Australia hosted the Asian Cup and the domestic competition was forced to stop to give it the stage. There will probably never be a tougher season for an A-League club than the one Wanderers has experienced.
It is no surprise that, under the circumstances, Wanderers is battling to avoid finishing last.
The club has never complained too loudly about the scheduling, but the situation with Perth being penalised for cheating the cap but not finishing last - in a season during which Wanderers had no choice but to put up with nightmare scheduling, ruining its campaign - is a different story.
Wanderers chief executive John Tsatsimas told The World Game he was angry about the situation.
"It is difficult to reconcile how a compliant club like the Wanderers, or Central Coast Mariners or Newcastle Jets, can be viewed in a different light to a non-compliant club and be forced to finish below it on the competition table," Tsatsimas said.
"If the Wanderers had the benefit of the same resources as Perth apparently did this year, it would only be natural to assume we would have been done much better as well, so if Perth has broken the rules as is alleged, why hasn't it been penalised right to the bottom?
"If you finish last, it can affect your sponsorship and membership. If the allegations against Perth have been proved, it should be in last place."
The Wanderers club feels it has given its all, on and off the field, to try to perform as well as it can on behalf of the Australian game in Asia.
It would have had to simply accept finishing last - if that is where it finishes - had the extraordinary drama surrounding Perth not developed, but under the circumstances it feels it should not be at risk of getting the wooden spoon when another club has been found guilty of cheating the cap.
Glory abandoned its appeal bid and accepted the penalties of being banned from the finals and fined $269,000 after receiving notification it would be issued a third show cause letter from FFA.
That was related to FFA uncovering evidence of further payments and benefits that allegedly weren't disclosed, to the value of $100,000. Even before that, Glory was found to be $400,000 over the $2.55 million cap for this season.
One of the star players Wanderers lost at the end of last season was Youssouf Hersi, who joined Perth.
Wanderers has been forced to stretch the limits of its playing roster, delving into the youth-team group, just to get through this season.
After Sydney FC's 4-3 win over Newcastle Jets on Friday night, the battle to avoid the wooden spoon will definitely go right down to next weekend's final round.
Ahead of playing its round-26 game at home against Adelaide United on Saturday night, Wanderers was in last place on 15 points - two points behind ninth-placed Newcastle.
They are the only two teams in the running for the bottom spot. Central Coast will finish eighth regardless of results in the final round.
Newcastle is away to Brisbane Roar on Friday and Wanderers is at home to - of all teams - Perth Glory, on Saturday.
