Yes, if the slots aren't lining up properly, this is a warning indicator that you have the motherboard mounted improperly. Find out what is going on and get it straightened out BEFORE you apply power, or you may end up with a direct to the case short and burn up something!
Make sure you find every screw hole in your mobo, count them up, & match them up with the holes in your case. Put one of the brass stand-offs in each of these holes to correspond with the screw holes in your motherboard.
DO NOT put any more brass stand-off's than your motherboard will support. If your mobo has 9 screw holes put 9 stand-offs in the case to match these holes exactly. If you have to make a paper diagram then do that.