unexpected input at Nios core!

Semir,

By chance are you using any kind of pre-release or beta? We screen for such signals 'popping out the top' quite thoroughly in anything nearing release although its not uncommon in our development work to see them as new logic is being added (basically it means that an internal signal is not driven by other logic as it should be).

If you are using a released version (1.0/1.01) of the Nios II kit I'd reccomend that you contact Altera support and explain the problem along with your system's ".ptf" file so that they can file a report on this.