How does the political party system contribute to conflict between the president and congress?

People within the same party don't necessarily hold exactly the same views. At this point, that's especially prevalent within the Democratic Party because over the last few years the Democrats have generally been more accepting of variation in their members' views (whereas Republicans who disagree with the party line tend to end up losing their jobs or being ostracized by the party--see US Senators Michael Bennett and Lisa Murkowski, Florida Governor Charlie Crist, Representative Mike Castle, etc.) At other points in US history the reverse has been true, but there is still always some level of disagreement among different members of the party, so there's bound to be some conflict.