In this case, you should look carefully the ports that are not connected. If it is the pins left for scan test i.e test_se, test_si, test_so, the problem will be solved after the scan insertion. In some other case, the pins are left there for extendablity or some other purpose, and you know that, that's also ok for you.
MAKE SURE each unconnected pins are acceptable in your mind. LOOK CAREFULLY, What if you forget to connect the clock on the top of the design when your boss are calling you or you are on the last working day before vacation?
Unconnect pins are cheap but expensive when it is an unwanted one.