Memory verification issue

For the timing requirements, check that all your inputs/outputs and clocks are properly defined and that you don't have any critical warning from timequest. Having a look at the timequest user guide (http://www.alterawiki.com/wiki/timequest_user_guide) may be of some help here.

I think you are right about the software size, and the remaining of the memory will be used for heap and stack. The application could crash if there isn't enough free memory available, but I don't think it would cause a verification fail.

I think I would look for a bad timing problem first.