I recognized that before Cyclone V FPGA device being initialized (immediately after power-up) there is some voltage on its IO pins (not Z-state that expected). How to prevent appearance of these parasitic signals that cause PCB problems?
As per the cyclone V power management guidelines.
the Cyclone V device does not drive signals out before or during power up, the device does not affect the other operating buses.
Page no: 317
And I felt like may be the below scenario could have happened
device uses GND as a reference for hot-socketing and I/O buffer circuitry designs. To ensure proper operation, connect GND between boards before connecting the power supplies. This prevents GND on your board from being pulled up inadvertently by a path to power through other components on your board. A pulled up GND could otherwise cause an out-of-specification I/O voltage or over current condition in the Altera device.