The match looked to be heading for a draw until substitute Garnacho ran clear of the Gunners' defence in the 88th minute and slotted past Aaron Ramsdale.
However, VAR ruled the possible match-winner out for offside following a check as the young Argentine strayed centimetres beyond the last man.
Declan Rice and Gabriel Jesus then scored in injury time to secure a thrilling win, leaving Ten Hag to claim the VAR decision was incorrect.
"It's not offside - it's the wrong [camera] angle," Ten Hag told Sky Sports.
Ten Hag also pointed to a possible foul by Gabriel on debutant Hojlund in the penalty area before Garnacho's disallowed goal, which VAR also checked, and claimed Johnny Evans was fouled before Rice scored.
"There was a penalty on Hojlund, and foul on Evans [for the Rice goal]. The performance was right. Everything went against us,” he said, before adding to BBC Sport on the Rice goal: “It can’t be that this goal is given. It was a clear foul.”