The beliefs and ideals that you hold as individuals don't gel with each other's, but you might not really feel the effects of this until well into the relationship. You could think that there's a lot of commonality between you until your bond has a chance to mature, and then the cracks start to show up. You both have well-formed opinions on the big issues in life -- religion, spirituality, morality, politics -- and you find that you disagree on many of these subjects.
Depending on the strength of the rest of your relationship, this could be a huge problem between you or it could simply be an irritating divide. For example, difficult communication makes these problems nearly impossible to deal with, because you aren't able to talk them through without getting into a fight and accusing each other of being flat-out wrong. But who's to say either of you is wrong when it comes to such subjective beliefs? If you find yourselves pointing the finger at each other in this way, you're wise to take it as a sign that you're reacting against the vulnerability that these fundamental differences cause within you. Compromise is necessary in this case, but could be exceedingly difficult without good communication and mutual respect working in your favor. If you're able to accept the differences between you and not feel threatened by them, they shouldn't cause huge problems in your relationship.