In the original draw, Rangers were announced as playing against Aberdeen, while Hearts were due to face Dundee United.
The Scottish Football League has since written to the clubs to notify them of the mistake.
But Dundee United chairman Eddie Thompson is furious with the mistake.
Thompson told BBC Sport: "It's a total farce. I've spent four hours on the phone with Hearts arranging when the game would be played, where the game would be played and so on.
"I'd like to know what the SFL have been doing for four hours between 1330 GMT when the draw was made, and 1720 GMT, when they notified us of the mistake.
"It was a member of the media who contacted me long before I heard from the SFL and I thought he was off his head."
Presiding officer Ferguson added: "We have worked as quickly as possible with the Scottish Football League to resolve the situation.
"As a life long Stranraer fan, I think everyone can be assured that there was no ulterior motive."
David Longmuir, chief executive of the Scottish Football League said: "The SFL has a duty to the teams involved to correct the error and to protect the integrity of the draw."
When asked why the draw was not redone, Longmuir told BBC Sport: "We looked at all the options.
"But we felt the draw was done in the proper manner and decided to stick with the sequence in which the balls came out."
First Minister Alex Salmond helped make the draw, televised live at lunchtime on BBC Scotland, and he said: "As soon as the mistake was realised Alex Fergusson did the right thing by owning up and moving to correct the genuine error straight away.
"Once football fans are over the shock, I am sure even Hearts fans like myself will have a wry smile and get down to planning for the semi-final."
The Rangers versus Hearts match will be played at Hampden and the other tie could be staged at Tynecastle or Easter Road.
The ties will be played on 29 and 30 January, although it has not yet been confirmed which matches will take place on which night.
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