DDR2 Controller for Cyclone II

You can't just connect "some" of the read data to pins.

Consider this. What is the purpose of putting a DDR2 memory controller in the project if it's not attached to anything? So Quartus in it's intelligence says "Oh these DQ pins don't actually connect to anything in the design; I might as well get rid of them". So it does. Then Quartus flags an error for the DQ logic saying that it's not connected to anything.

Solution:

Don't put an unused memory controller in the design. If you want to do a test compile, use the example driver to verify the controller.

Jake