If IPing endogenous proteins, antibodies most often recognise a native protein, and therefore one is not able to include a denaturation step. Current iCLIP conditions are optimised for use of such antibodies. While the washing is as stringent as possible, it will not disrupt very stable RNP complexes. Therefore, there is a chance that you will co-IP other RBPs, and RNAs that stick to the beads or are non-specifically bound to your RBP.