DDR3_CONTROLLER problem

Are you sure the dynamic control should be ground? If you did not chane it, then ok

Next thing, the error means that component there, is making an illegal conection, perhaps it is bidirectional and it is connected to something unidirectional outside. Perhaps it is connected to the wrong type of pin, perhaps it is connected to multiple pins outside on your top level (note that the second error says it "also drives out other destination than the buffer").

Here is the help saying what that means:

http://quartushelp.altera.com/13.1/mergedprojects/msgs/msgs/escl_scl_illegal_wys_io_ibuf.htm

Perhaps one of these gives you a hint, someone had this on a Stratix IV part:

http://www.alteraforum.com/forum/showthread.php?t=5825