I know you can have either a Well or a Water Mill (although that depends on whether a river is present; no city has the option to build both). You can also have either a Train Station or a Seaport. Although again, Seaport depends on being on coast and (I think) Train Station depends on a rail connection to the capital. But I think a coastal city does have the option to build either one (but not both) if the prerequisite of a rail line is in place. Are there any other mutually exclusive building pairs?