as long as the bolt threads in far enough to clamp the head down and not bottom out it is fine. once in a while there is core shift during the casting process and the wall is thick near the deck. when the machine drills the holes it only drills so far and leave a buttress at the bottom of the hole. as long as it is deep enough it is fine. also check the head bolts to see if one has been shortened??
Measure the thickness of the head @ that bolt location, add the thickness of the head gasket. Leave the head off & screw the bolt in the subject hole by hand.
Measure from the deck to the underside of the bolt head.
If the length of the protruding bolt is less than your head / gasket measurement your good to go. If no add a cut washer to the bolt or trim a few threads off the bottom.