It is possible that the algorithm that identified these over pricings since season 1 has not kept up with the general development and improvement of player quality. The result would be similar to your situation.
IMHO you should be able to sell any of your players for any amount of money... however, due to the amount of cheats that try their luck here (amongst many awesome people) i can understand GKO limiting the ability to sell bad players at high prices to ghost teams. If you look from a different perspective you could also argue that it helps smaller teams compete in the transfer market with managers being scared of selling their player for 'too much'.
The only real soulution to stopping genuine players getting caught in this web is to introduce proper player prices, then to put a sensible percentage cap depending on CA/LA/PR. This would be a rough example...
Player value 300000G... CA 3/LA 5/PR 3 would allow you to add 20% so maximum sale price 360000G
Player value 600000G... CA 6/LA 10/PR 6 would allow you to add 40% so maximum sale price 840000G
This would keep lesser players more attainable for lesser teams and better players only available for better teams, its not like Messi would ever be playing for a second division team... so why in GKO