What to do when research is ending up in useless clinical trial
The problems you indicate should result in non-replicable results. The way this can be shown is repeat the published experiments as closely to the published protocol as humanly possible, with a correct design, carefully documented, etc. etc., and get different results. That is a publishable result. 

Whether such a replication will somehow violate your confidentiality contract is something you need to discuss with a lawyer. My feeling of justice says that it should not violate that, but justice and law are two very different beasts. 

Just writing down your experiences, risks ending up in a "he said, she said" situation, which is not going to resolve anything. Moreover there is the legal aspect of you signing a confidentiality contract. Anything legal needs to be discussed with a lawyer, not random persons on the internet.