The truth table is for a slice in time. So the truth table for an inverter tells you that when the input is high the output will be low and when the input is low the output will be high. As you are seeing though many circuits are pulsed, so when the input pulses high, the output pulses low and when the input pulses low, the output pulses high.
Depending on the circuit, and the logic probe, the reading should show up as low--pulsing high or high-pulsing low. With the opposite reading on the output of the inverter. Of course this doesn't apply on circuits where the low and high pulses have the same duration.