It is true, but a losing battle! With things like systems on a chip, mixing of RF, analog, digital, optical on a chip, you are simply entering the realm where no one person is going to have a clue how every part of a system works. There will be a team of engineers, and hopefully you can iron out the interfaces between your individual areas of expertise.
But, in the area of Microwaves, sure, the computers lie to you all the time. In fact, most computer simulators are written by programming geeks--not microwave engineers. So their software is ALWAYs suspect!
This is all complicated by the fact that microwaves are NOT intuitively obvious. If you took up woodworking for a hobby, for instance, it is pretty easy to see how the wood responds to your chisel, and the right and wrong way to work it. In microwave engineering, you can not "see" the electrons dancing along the transmission line. Only after many years of simulating. testing, and troubleshooting various designs will you develop that intuition. But after that, thing make perfect sense.