There are many different ways.

Some take pictures of objects, usually certain bright asteriods. There is
also a world network of recievers working like opposite to GPS.

Does anyone know how we navigate our deep space probes? I know we use
radar and GPS in LEO. What do we use for deep space? My guess is we use
Doppler shift a lot -- but that is just a guess.

My understanding is the navigation system of the probe that had the unit
conversion error was "telling" us that there was a problem, but we didn't
have enough confidence in the navigation system to realize there was a
catastrophic error in the trajectory.

Since the way they pass from one peice of software to the next and there
errors were all in that software as well no-one thought better.