What could cause an alignment problem after crowning?

Crown too high: In most instances the crown is too high thus, causing your tooth alignment to become uncomfortable. This could easily be corrected by seeing your dentist to adjust the occlusal interference and thus, improving your alignment.

Size: Crowns are made for the most part in freehand, so during the cementation process, adjustments are normal. Additionally the marking paper is not necessarily more accurate than what you feel. I suggest you tell your dentist your concerns and maybe more adjustment is needed on your crown. It's common for a crown to need an additional adjustment after cementation.