That goal sparked a period of domination from England and they made it 2-0 just before half-time through Ellen White, but Scotland were a different proposition after the break and pulled a goal back through Claire Emslie in the 79th minute.
Kerr said she was disappointed at the penalty decision but conceded her side were well below par in the first half.
"It's a hard, hard job for the officials, and that's what VAR is there to do, to help them. By the letter of the law it's a penalty but I thought it was harsh," Kerr told reporters.
"If it had been the sole decision and (the game ended) 1-0, then I might have felt worse ...
"You just have to try to react to those decisions and try to get your game plan right after it, but we did lose a bit of momentum."
Kerr said Scotland were outgunned in midfield in the first half and that they would have to analyse what they could have done better.
"Firstly we need to look at the first half, where things went wrong. We are playing at a World Cup and we need to scrutinise that because we weren't at our best," she added.
Scotland next face 2011 champions Japan in Rennes on Friday and Kerr said that despite opening Group D with a defeat there was plenty to like about her team's display in Sunday's game.
"I think the biggest thing for us now is that we need to recover because that was a tough, tough game and we are going to face a tough Japanese side as well," Kerr added.
The Scots round out the group stage against Argentina in Paris on June 19.
(Reporting by Peter Rutherford in Seoul; Editing by Nick Mulvenney)
