Same logic high ,but different voltage

Sounds like you are referring to a specific Dev Kit (e.g. C II Nios II board). Unfortunately you didn't yet tell. A 5V pin at a particular GPIO isn't directly connected to the FPGA, these Dev.Kits have additional circuitry between connector pins and FPGA, and also additional devices connected to some of the pins. In this case, the reported "1.14V" is meaningless without telling the exact DevKit and connector pin locations.