Dual port memory corruption

What might be happening is without constraints the fitter is putting most of it's effort into paths that are failing due to a lack of constraints and causing other valid paths to fail in the process. The fitter optimizes based on slack times so if you had some paths that should be false paths and they have the worst slack times due to a lack of constraints the fitter will work extra hard on those paths. So it could be the fitter was working hard on improving the slack time to LEDs instead of focusing on on-chip paths like between Nios II and the dual-port RAM.