Being incompatible doesn't mean your relationship must end, but you'll need to address some things.
After a few months, you may notice some differences that indicate to you the partner you found is not the person you thought they were after all. In most cases, this is simply because everyone is on their best behavior when they meet a new person. They're showing you all their good traits and pleasant attributes.
However, once people start to get familiar and comfortable with another person, they can lapse into their real personalities. This isn't always a bad thing, though. You might find you like each other more once you drop the pretense of always being perfect.
Of course, you could learn that you don't like the stranger who emerged at all. Incompatibility doesn't always mean that you have different goals or hobbies or interests. It could mean you have different objectives in life or different religious beliefs or any number of things.
Being incompatible also doesn't mean your relationship has to end, but there will be some things that need to be addressed.
The level of incompatibility between you and your partner is something only you can know. Some couples agree to be tolerant of the other's beliefs or goals. Other couples make the change to one or the other person's way of thinking.
Unfortunately, there can be much deeper issues to overcome if your partner doesn't want any children and you want four, plus a dog. Your partner might be into sexual fantasies that involve rubber chickens and gummy bears—or any other array of props—and you just can't bring yourself to go there.
Your partner may also have issues with substance abuse, physical abuse or other deeper psychological issues that you don't want to be a part of. These deeper incompatibility issues can be reason enough to consider looking for a new partner.
Being incompatible on some issues doesn't mean the relationship needs to end. You may simply need to work on communicating your needs and preferences to your partner. However, when there are deeper issues involved, it may be time to question whether you're happy enough to compromise your own values for the sake of a relationship.