This story sports an interesting variation on the mind projection fallacy anti-pattern. Instead of confusing intrinsic properties with those whose observation depends both on one's mind and one's object of study, this variation confuses intrinsically correct conclusions with those whose validity depends both on the configuration of the world and on the correct interpretation of the evidence. In particular, one of the characters would like the inhabitants of the simulation to reconstruct our modern, "correct" scientific theories, even though said theories are in fact not a correct description of the simulated world.

Here is a relevant (and spoiler-free) passage.

[The simulation's] stars were just a planetarium-like backdrop, present only to help [the inhabitants of the simulation] get their notions of heliocentricity and inertia right

The mistake, of course, is that if the simulation's sun is merely projected on a rotating dome, then heliocentricity isn't right at all.

edit: it turns out that Eliezer has already generalized this anti-pattern from minds to worlds a while ago.