You may need to move the pins around. Or upload your project here for others to check .
So PSoC devices have a routing fabric. In PSoC 1 you had to manually define the routing. For PSoC 3/4/5, PSoC Creator allows you to make a logical connection and then attempts to map that to real hardware.
So your first thought may be, well that's silly I can route things myself. Trust me, you can't. For complex designs we're talking about thousands if not tens of thousands of connections that have to be correct while optimizing for timing requirements. It is a NP problem, not easily solved by a computer or a human.
So PSoC Creator has a router which takes your logically connectivity and maps it to the physical chip, which is good. That said, since you're defining things logically, you can make a design that won't route. It isn't detectable until the router runs, but like I said, routing is a hard problem, so that is deferred until you build. (If the router ran every time you made a change, you wouldn't be able to use the tool, it would simply be too slow.) Your logical design does have some DRCs, but that doesn't mean the design is feasible. In some cases the physical block simply doesn't connect. In others you've put too much in the design to have it fit.
Since you're talking PSoC 4, it is more likely that you've connected a fixed function block up incorrectly. Probably a component using the SCB or TCPWM. Check your pin settings carefully.