Play was held up whilst Scunthorpe fans entered the pitch from the Doncaster Road End terrace, with only minutes to play.
Swindon manager Kevin MacDonald hinted the hold-up may have played its part in the way his side collapsed late on.
“Whether during the delay we lost our concentration a bit, I don’t know,” he said.
“But our play warranted a better result than that.”
Despite the victory, Scunthorpe were still relegated to League Two.
Tensions had been running high all afternoon, with both sets of fans clashing in the Clugston corner, before an hour long stand off in the car park.