I've got these out on mine at the moment. The rear frame will drop slightly when you take them out and by the looks of things you possibly aren't actually engaging the threads in the case becasue the bolt holes arent properly lined up. The bolt is pushing up against the case, just (literally just) below the bolt hole (if that makes sense).
1. Don't force it. If its not going in, its not going in for a reason.
2. Remove the bolt and make sure it is absolutely clean. WD40 them clean. If you galled the threads on the bolt, then suggest taking a bit of time to clean them up again. Its an M10 x 45 bolt so if you have an M10 nut handy, you may want to run the nut down the thread to make sure the threads are good. if you have damaged the threads and can't clean them up, have a bit sigh and a talking to yourself, and order some new ones.
3. With the bolt removed, just make sure the subframe and case holes line up properly. You may have to lift the subframe slightly to do this (I do on mine - by about 5mm or so). I think this is probably the real issue.
4. Possibly loosen off (but don't remove) the other two bolts holding the foot peg bracket in place (as Flatdog suggests)- allowing that a bit of movement may take the pressure off the M10 bolt you are trying to insert.
5. if you have also removed the other bolt on the other side, you may have swapped them over and weirdly, one will go in one side, but doesn't fit the other side so well.
6. If you have mullered the case, nows the time to remove the bolt and go and get an M10 tap to recut/cleanout the thread really, really carefully, whilst some of it still exists...
Hope that helps.
H