I highly recommend reading this article:
https://onemileatatime.com/boeing-737-max-lion-air-simulator...
The first crash was with Lion Air. Boeing mocked them for wanting simulators. After the crash, Boeing claimed pilots of Lion Air were at fault. This while saying no simulator training was needed.
These were the conversations of two employees. I wouldn't say that Boeing outright mocked them but, in the processes going on above the employees paygrade, simulators were difficult to get to Lion Air
Boeing employees should be in prison, there shouldn't be bail while awaiting trial. This is a act of willful negligence and deceit and coverup that killed hundreds of people. It's one of the biggest crimes ever in the history of our country.
I was surprised to learn that at least at that place, the actual aircraft software was running in the simulator, and that external sensor inputs to the software were being mocked out.
It was surprising to me because I had never thought of a simulator as simulating the aircraft itself, but rather only the experience of flying it.
So from this, I don’t think it the case that a simulator is having trouble recreating flight characteristics or reimplementing a ‘bug’ or other behavior because my guess is they are not reimplementing much/anything on the software level.
Though your point about bugs only surfacing after many hours of continuous operation could theoretically still occur without further controls, and of course it is hard to make a mock full-fidelity, especially so in the context of a full suite of analog flight sensors/actuators.