Fans have questioned why no one has realised the pair served in the army together, but the producer has finally debunked the alleged "plot hole" on Newsnight.
Andy took his own life during the second episode, after David discovered he was the sniper trying to assassinate Home Secretary Julia Montague.
After the tense scene, viewers began to speculate whether David and Andy had met each other previously in the army – but Jed has now silenced the rumours.
He told Kirsty Wark of their friendship: "That's something that was planted in the series and it has taken a considerable time to resolve that stay.
"Although there's a thought they were in the same battalion they weren't. I don’t know where that's come from.
"They simply served together in a very big war at the same time but they were in different regiments."
The hit BBC series will come to its dramatic end this weekend, with viewers hoping Julia's death by bomb explosion will be solved once and for all.
After five episodes Budd has failed to prove that he is innocent, and he has kept numerous things from his team, including his affair with Julia.
However, a sneak peek from Sunday's episode sees the finger of blame turn on Commander Anne Sampson, as she is seen looking very uncomfortable when her connection to crimelord Luke Aitkens is revealed.
Despite this, many believe that Julia isn’t dead at all, a theory that was fuelled by Jed himself earlier this week.
The series has been branded the "best drama in 20 years" by fans, and Jed recently revealed he is already in talks with the BBC about a second series.
However, the writer gave viewers another cryptic clue about the finale by claiming he will definitely invite Richard Madden back to the cast, "if David Budd survives."
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