Approaching half-time, the winger was brought down by Nico Schlotterbeck in the Dortmund half but the referee waved played on.
Just moments later, the German defender ran to the left-hand side of the Newcastle box and assisted Felix Nmecha's cool finish.
The goal was allowed to stand and therefore give the visitors a precious lead at half-time but fans were left wondering how.
Replays show while there was contact from Schlotterbeck, the tackle was very clean, however, Gordon's shirt was tugged by Marcel Sabitzer moments before.
Taking to X, one said: "That's a f****** foul on Gordon he got pulled back."
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"Surely the ref brings it back for a clear foul on Gordon?" added a confused second.
A third said: "How's that not a foul on Gordon? Twice the ref hasn't called a foul and Dortmund have countered, first nearly lead to a goal and now they scored with second. UEFA really don't want Newcastle progressing."
"Had to be a foul on Gordon before the second tackle," said a fourth as Newcastle trailed at St. James' Park.
Dortmund could have taken the lead in the opening few minutes but were denied by an excellent double save from Nick Pope.
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However, Nmecha's strike proved to be the winning goal for Dortmund as they picked up their first victory in the group stages.
Newcastle did threaten themselves but couldn't find the target as the rain poured down on their home turf and they fell to defeat.
The Magpies also had to deal with an early injury to Alexander Isak, with Callum Wilson replacing him but failing to make an impact.