The Doncaster Rovers boss thought his side were in control at 1-0 up and the first penalty – awarded midway through the second half – changed the momentum of the game.
Wellens accepted that Kyle Knoyle’s challenge on Ryan Broom probably was a foul.
But he accused Kieran Agard of diving to win the second penalty in stoppage time after a coming together with Rovers goalkeeper Pontus Dahlberg.
“They wouldn’t have scored apart from a penalty or a counter attack,” said Wellens.
"Second half, up until the penalty, we were in control.
"When you get to the Premier League they have VAR. They [referees] don’t change the momentum of the game. Referees at this level change the momentum.
"There’s been nine yellow cards today. Nine! There’s not been one bad tackle.
"There’s not been a touchline altercation. It was very respectful between the fourth official and myself and myself and Lowey [Ryan Lowe, Plymouth manager] who I’ve got a lot of time for.
"My kit man text through ‘Who’s the referee?’ beforehand. It’s a running joke. No one wants him [to referee their game]. It’s been like that for years and years.”