Do you really know each other as well as you think you do? This is the question you both have to ask yourselves as your relationship progresses. In the beginning, when you were first getting to know each other, there could have been a lot of philosophical or spiritual talk, exchanging of ideas, comparing of notes.
You probably feel uplifted by each other -- here is someone, you think, who's right in line with what I believe! Unfortunately that isn't exactly true. The more that you idealize each other, the harder it is to see the differences between you until it's too late -- meaning, when those differences hit you over the head in an unpleasant way, because you're finally unable to ignore them. Now, don't misunderstand -- a certain level of idealism in a romantic relationship is actually preferable. It helps create that loving feeling of awe and excitement that keeps your romantic feelings alive. However, when it starts to obscure the individuals that you truly are, that's when it becomes a troublesome influence. You could react very strongly when reality starts to intrude, having fights over your differences in spiritual or philosophical beliefs -- differences that have been there all along. The differences themselves shouldn't really cause problems; it is your emotions about the differences that are hard to handle, unless you can force yourselves to deal with each other more honestly.