Hi and welcome to the forum. It is tricky to get the hinges right but I am surprised the instructions are not clear. I have just fitted a hinged roof to my bakery,( no pic yet, sorry) and the instructions were very clear. However my hinges were butt hinges not cranked for the roof. One thing to check is if the holes are clean.
MDF has a habit of rising up out of the hole as you tighten the screw home. This makes the hinge itself rise up and not fit properly. We took the hinges off again and cleaned around the hole with a blade. Also the countersinking of the screw head is deeper than that in the hinge causing the screw to bind on the wood. Correct it by countersinking slightly the hole in the wood to allow the screw to go fully home.
Sorry not to be of any more help. Can you post a picture of the problem?
Sue