why didn't the brownie bake when cheesecake was put on top?
One thing that can matter is that darker pans often absorb more heat (from  radiative heating). So if your 9x13 pan is dark-bottomed (e.g., nonstick, or darkened from years of use) it'll run hotter than a shiny foil pan. I'd be surprised for that to result in raw, though, normally its just more or less browning.

If you put a baking sheet under the foil pan, that could also function as an insulator, especially if its a steel pan instead of aluminum.

I'd guess instead some other "human error" thing happened: measured and ingredient incorrectly, left something out, added something twice, set the oven temperature (or mode!) wrong, etc.