Can't speak to overall issues, and haven't watched it since it originally aired, but there was somewhat infamous friction between Julianna Margulies and Archie Panjabi, to the point where they would not appear in a scene with each other. The scene in the final episode (or near it, I don't exactly remember) in which they appear together at the bar is assembled from separately shot footage.

I think it mostly suffered from the standard network TV show issue of not having a real plan beyond "as many episodes as possible".