Hi Jules
I am so sorry to hear that your son is not a happy camper.
I know all about that feeling! My son went to a creche that i will never recommend, EVER!!! My son did the same, my biggest problem is that it happening in view of anyone. (they had cctv cameras and every now and then i would log on at work and have a peep at to what was happening, i was not happy at all!) We did move him one day and i never looked back. so yes, i would say that there is a problem.
I found a new creche and i will never look back, my son (just turned 5) is in the creche even before i lock my car, he runs in everyday, i dont have a problem with him crying or not wanting to go to creche, sometimes he wakes up on a Saturday morning getting ready for creche (getting creche clothes on) eager beaver. Yes sometimes we have the odd say where he wants to stay with me or asks to go to granny.
Shame man. Good luck.