In the 40k Universe, the foundation of humanity is based on faith in a fair few things, much like a fairly unstable stack of pebbles - each piled up into a tower. Move one, and the whole thing comes tumbling down.
At the core of it, The Emperor, and the Adeptus Mechanicus. These determine what is heresy, based on their own judgement of what is pure and impure; and this is what humanity follows. any thought that challenges these laws is considered heresy.
One such Heretical text, on which the Logicians have based their belief systems, is In Defence of the Future: A Logical Discourse, which discusses the abandonment of current practices and teachings, and developing things anew. Basically (from what I gathered); "Stop recycling - everything is getting old and rusty. Melt it down and start over".
Looking into it a little deeper however, the main point is that the Logicians argue that they believe their teachings are the correct path, and this means that they, in stead of the Mechanicus, and the Emperor, should rule. Apart from this, the only difference is that instead of maintaining humanity's domain throughout space by use of old, rusted equipment, they should take back what is lost, and expand once more, taking dominion over all.
So fundamentally, the main issue I see with the Heretical status of this text is that it has led to a Cult believing that the emperor and the Adeptus Mechanicus should be removed. Is this correct, or am I missing something more?