One of their problems was that the Revolutionary regime didn't trust the Army. Interestingly,the Pasdaran didn't use ways to pass important information,that could be decrypted. They used people to pass on important messages to officers and units.
They did that because they didn't want the Army to know their moves,but it turned out that Iraqis too didn't know the Pasdarans' plans and operations. They did manage to decrypt and intercept plans of the regular Army often,but they couldn't figure out the IRGC,because of that tactic.
Now,yes the two of them didn't cooperate well and often and that was problematic for Iran. The other reason for their massive casualties was that Iraq had crazy defences around Basra and Baghdad and they couldn't take these cities. So it was like a stalemate. Of course,Saddam used chemical weapons too when Iranians were going to overrun important defences inside Iraq.