you don't have the transmission shaft all the way in the pilot bearing in the end of the crankshaft if it is a stick shift, if an automatic trans, it's not in the converter all the way... BOTH WAYS WILL SEVERELY DAMAGE THE TRANSMISSION AND MORE.
STOP!! DO NOT FORCE ENGINE TO TRANSMISSION! If it does not mate up flush, something is wrong. Like he said above, if it is automatic, the torque converter is not properly installed all the way in. If you have forced the bolts to draw them together you may already have damaged the torque converter and front pump of the transmission.