Madrid were adamant they should have had a spot-kick when Karim Benzema's cross struck the arm of Betis defender Zouhair Feddal, who had slid in with his right hand trailing behind him.
Referee Jose Maria Sanchez Martinez consulted with VAR but did not go to a pitch-side monitor to check the decision himself, much to Madrid's chagrin.
Having been handed no reprieve by the officials, Madrid upped the pressure, but Joel Robles stood firm with two fine saves from Vinicius Junior, with earlier missed opportunities coming back to bite Los Blancos as Zinedine Zidane's side missed the chance to move top of LaLiga.
Courtois, however, did not entertain the possibility the referee was responsible, even though the Belgium international believes Madrid would have been worthy winners.
"It is not a penalty. The handballs in the [penalty] areas are very complicated," Courtois told reporters.
"It is not easy for referees and players to know when it is or not. We saw something, but we cannot protest something that no longer exists.
"I think in general we had a good game. We have created many chances. It is a shame, but we must continue. I think we played a game to win. You can't take anything away from Betis."
Zidane echoed Courtois' sentiment, claiming he could see little fault in his side's performance even though Madrid failed to capitalise on Barcelona's defeat to Levante and Atletico Madrid's draw with Sevilla.
"There was a handball, but the referee has decided it was otherwise. I don't get into referee issues. I saw the handball, but the referee's interpretation was different," Zidane told a news conference.
"The criteria for handball is clearly that of the referee because he has not consulted VAR. You have to respect what he says.
"At the level of play, intensity and attitude, everything was perfect. We were missing a goal. You cannot reproach anyone. We tried until the end.
"Everyone fails. It's going to be a very complicated league."