Usually you write a simple model, it does something pathological like diverging to one extreme, you maybe tune the parameters a bit until it does something that fits better with your expectations, then you publish. But the behavior you observed is still pathological, dependent on fine tuning of the model parameters, and has nothing to do with the relationship between the model and reality.
I especially panicked when I saw people on HN arguing we should drop all those SIR-based models for Covid-19 and use multiagent simulations instead.
Also, NetLogo obfuscates from you that usually what you're trying to model is a very simple one-dimensional equation that could be written in three lines of Python, and that you could see the problems with immediately if you'd look at the actual equation.
This is a good example: https://arxiv.org/pdf/1802.07068.pdf
My own review is in Hebrew, but it seems like this is a good one: http://joshuaballoch.github.io/luck-in-life-still-misunderst...