Both players posed for photos holding United shirts with Ferguson, while Ljajic, who is regarded as one of Serbia's brightest young talents, made several trips to Manchester to train with the squad at their Carrington base.
But having assessed Ljajic's performances United decided they had better midfield options already and withdrew their interest.
"We have a platform that allows young players to develop and get into the first-team," added Phelan.
"We looked at Adem and he has the potential to do that.
"But sometimes you cannot fight these things. Sometimes you can get work permits, other times you can't. Adem fell into the latter category, which is why we made the decision."
Critics of the Glazer family's ownership of the Red Devils have claimed the decision not to sign Ljajic was down to £790m debt the club are in.
Duncan Drasdo, chief executive of the Manchester United Supporters Trust said: "Whatever the reason for the Ljajic deal falling through, the fact is with the revenues flowing into the club, we should be competing with Real Madrid and Barcelona for players of the calibre of Messi and Kaka."
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