When installing a motherboard to case standoffs, the best approach is to start all screws a couple of turns, and leave them loose. When all screws have been started properly, give each one turn, then press on the front edge of the motherboard in such a way as to move the motherboard evenly toward the back of the case, while maintaining parallel between the back edge of the motherboard and the inner rear surface of the case.
From rear to front, tighten the middle MB mounting screws. Tighten the rest of the screws in side-to-side pairs, from rear to front.
If you can't get every single standoff to align with every hole, on a nine-hole motherboard, examine the possibility that the standoffs are improperly placed. If there are no threaded standoff holes to allow for correct placement of all motherboard standoffs, seriously consider returning the case for replacement.
Non-proprietary motherboard mounting hole placement adhere to standards of location, and case manufacturers would do well to meet those standards.