are they covered by the shield somehow or is the angle made to difficult by the edge of the case.
There should be one mounting screw either side of the shield and in my experience the screw closest to corner is the hardest to fit. Try fitting these two first but obviously don't tighten them yet until rest are all in place.
Some, not all (self included) use a short magnetic screwdriver for the difficult placements on mobo. Just don't use it on your hard drive.
Most professional do not recommend their use at all but I've never had problem with at least 50 different mobo's over the years. Many will report the same.
i see they don't line up with case spacers. In the second photo it looks like shield is preventing the mobo from sitting far enough back. It is especially noticeable on the ps2 connectors. they are not quite aligned and more recessed than they should be. With the shield removed does the board line up correctly on case spacer. It looks like the board need to move at least 3 mm back to line up correctly.
you mean return case under warranty. The easy answer is yes. If they replace the case the problem may still exist. So go for a refund or put the cost of this case against something else they have of equal value. They are more likely to the latter.
Thanks for your help im getting Corsair Carbide 300r. My system will be Asus M5A97 LE 2.0, Corsair Cx 600w, Corsair Carbide 300r, FX 8350, Asus Gtx 760, Toshiba 500gb, Crucial 1600 mhz 8gb and Cooler Master Evo 212.