I've just had a look at Paul Koo's Aventador DVD. That clearly shows holes for the hinges to fit in, and the notes make a reference to making sure that the hinges don't foul the firewall under the holes or the doors won't sit flush. It certainly looks like you've got a defective part. However, it seems strange that both sides are the same. I've not seen anybody else have the same problem.
Have you tried pushing with an pointed object or similar. Could it be a bit of flash over the hole? It does look quite thin on the photos of the parts. Unfortunately I don't have my kit to hand to check. It's 6000 miles away
It might well be worth a call or message to Hornby, although there are rumours that they have sold Pocher to a Dutch company. Failing that, can you drill out the holes, or grind them out with a Dremel or similar?