They were not happy with the BBC's portrayal of the schools as teaching anti-semitism and homophobia.
But their response does not contradict the program at all. They just said that it needs to be put in proper context:
Hamza Andreas Tzortzis, iERA’s media representative said, “The attack on mainstream Islamic speakers because they hold established theological views is making the job of community cohesion difficult, as is the constant misconstruing or lack of context with regards to their statements. The programme-makers would have been better served to look deeply into the Islamic scholarly tradition and its historical impact, and they would have found a beautiful model of community cohesion. For example it is a well known historical fact that Islam and Muslims for centuries have been offering protection to the Jewish community.That "beautiful model of cohesion" is that the despised Jews can be "protected" as long as they meekly accept their inferior status and pay the jizya tax to their Muslim overlords. But that is apparently in no way incompatible with schoolbooks that ask Muslim children to detail all the "reprehensible" characteristics of Jews, which seems to be an established theological view.
At least iERA didn't deny it.
Actual equal rights of Jews and Muslims living in the same society? That's crazy talk!
And don't even get the Muslims started on Hindus...