Do you really know each other as well as you think you do? This is the question you both have to ask yourselves, regardless of how far you're into this relationship at this point. In the beginning, when you were first getting to know each other, there was a lot of philosophical or spiritual talk, exchanging of ideas, comparing of notes.
Now, you still probably feel uplifted by each other -- here is someone, you think, who's right in line with what I believe! But that isn't exactly true. And the more that you idealize each other, the harder it is to see the differences between you -- and when those differences hit you over the head in an unpleasant way, you two have a hard time even trying 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. But when it obscures the people that you truly are, that's when it becomes a troublesome influence. You could react very strongly whenever reality intrudes, having fights over your differences in spiritual or philosophical beliefs -- differences that, really, have always been there. The differences themselves shouldn't really cause problems; it is your emotions about the differences that is hard to handle, unless you can force yourselves to deal with each other more honestly.