United received 24,000 tickets, and by Thursday had sold just over half.
The Trust's Nick Illingsworth told BBC Solent: "It is a disgrace seats will remain empty at a time when clubs need every penny."
The Football League has said some seats would not be sold for safety reasons, and no more tickets would be allocated.
The real losers are the youngsters of the area
Trust spokesman Nick Illingsworth
For the same reasons, any tickets Carlisle are unable to sell will not be offered to Saints supporters.
"From what I gather the authorities at Wembley don't feel they can separate the concourses," he added.
"But Man United played Aston Villa in the League Cup final recently and the stadium was full.
"I don't think there are many genuine Saints fans standing there saying: 'I went to every game and I'm missing out'.
Will the club get more? Millwall were allocated 49,000 so surely we should be able to get the same?
Southampton are a racehorse that does not like mud
"But the real losers are the youngsters of the area. How many local football teams of kids would love to go up to that game? They are the people who would have taken up the extra 10,000."
Saints boss Alan Pardew said: "Surely in a recession if you've an empty seat you want to sell it, but I'm not sure of all the reasons."
Source: BBC Sport
Source: BBC Sport