If it needs only a bit of push towards the back of the case to align the holes, that's fairly normal in most cases. What I usually do when building them is lift the mobo up a bit, put the screw in the hole and then start putting it down while pushing it towards the back end of the case. At some point you'll get the screw positioned to the anchor so that you can then while holding the mobo, screw the thing in place and then it holds it there so you can attach the others.
If however even one of them doesn't hit a hole at all then the layout of the anchors is something else than for a modern ATX form factor. Make sure to have a look under your board that one of the anchors isn't currently shortcircuiting your board (happened to me once, pretty mini-lightning and a loud pop from the case and dead parts, yay).