You're probably tapping a top-level bidir or output pin when compiling for a device family that's Cyclone III or Stratix III. Try disabling Incremental Compilation in the Settings menu. The problem should go away.
Your other options. Don't tap the pin directly. For a bidir, you can tap the ibuf in the post-fit netlist. It usually has the name <pin_name>~ibuf. For an output pin, you can tap whatever feeds the obuf, which usually has the name <pin_name>~obuf. Look at the post-fitting technology map viewer to see the fanin/fanout connections for the pin.