DE0 Cyclone V GPIO 1-Z switching, RN series

It sounds like you're expecting to see 0V when the I/O pin is tri-state. This is a poor assumption.

The RN (resistor network) is likely to be around 20-25 ohms and combined with the schottky diode these protect the FPGA I/O - to an extent. Typically, in normal operation, you can ignore these. However, when all you're connecting to the I/O pin is a scope probe, the protection circuit comes into play - along with the FPGA itself. All the small currents associated with each of these - the probe, diodes, FPGA - will contribute to the voltage you're seeing on the oscilloscope.

Probe the pin with a 10kOhm-50kOhm resistor connected between your scope probe and ground. Do the same with the resistor connected between your probe and 3.3V (assuming that's the voltage of the I/O bank in question). See what behaviour you get.

Cheers,

Alex