Helik was dismissed 42 minutes into his Championship debut for tripping Lucas Joao who was through on goal then, seconds after the hosts took the lead, Andersen was shown a second yellow card for handball.
Struber confirmed that both players would be suspended for Wednesday's trip to Chelsea in the EFL Cup but they are only expected to be given one-game bans.
Struber said: "Both decisions from the referee were OK. We have to accept them, but it is not easy. Both players are very disappointed. But they are great boys and great players. Sometimes it is OK that they make mistakes but today we paid a big penalty for their mistakes.
"They are very reliable players but they did not have the right balance in these moments. Maybe the communication between the goalkeeper and Michal was not on the highest level for the first red card.
"It's not easy for Michal to make a mistake in his first game in the Championship but I am 100 per cent convinced that he learns from that because he is a clever, smart boy and he is ready to help the team. We will be patient with him, help him and support him from the mental side."
Struber was pleased with his side's performance in the first half but frustrated they did not score goals when on top.
"In the first half we had the game completely in our hands. Every single player knows his task. We created chances but we need strikers who can score goals. This is a big signal that we need new players. Everyone understands that and we work very close together to find the right players."
Both goals came from set plays. Struber said: "This is very painful. I can feel it. It's a crusher. Every player knows we lost the game through set pieces and the red cards. For that I have no patience. It is very hard. Sometimes I have no problems to go home after a loss if I can look in the mirror and know we have a plan and we can trust in our style.
"From open play they had one chance, until the end. It is very disappointing that they scored two set piece goals.
"It is not an easy game to analyse because we had two players sent off which made it very difficult.
"The boys worked very hard in the second half and no one gave up. From the mental side, it was a very good performance."
Barnsley have now lost both Championship games this season without scoring a goal but Struber said the performance in Berkshire was an improvement on last week's 1-0 loss to Luton.
Struber said: "This is the not the way I expected to start. We made very good games, except Luton. We are going in a good direction from the performance side.
"We made very good games in the EFL Cup against Nottingham and Middlesbrough, but we must also be ready in the Championship."