I had the same problem. In my case the lack if alignment seemed to be caued by the fact that I jacked up only 1 side of the car at at time causing the engine to pull moro to the lower side even though the lower side already had the new motor mount installed. After putting jacks stands on both sides and some raising and lowering of the eignie the hole aligned enough for me to get the bolt in.
Also useful for this sort of thing is if you have a long tapered punch that will go through both holes. You shove it through the hole and the tapered part helps with the hole alignment.

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84 300D, 82 Volvo 244Gl Diesel