You are assumming they higher beings are functioning on timescales comparable to ours. Imagine a colony of microbes on an agar block writing out morse code intended for us - but there is no-one and the labs are locked for the night. Yet they keep trying for generations...
Alternatively - the spatial scales are very different and an entire galaxy or ours is not observable by their 'naked' eyes.
Sure, it really depends on the speed of the simulation relative to their own, and the level of resources poured into this (is it a high school project, or the combined output of their entire civilization? what do they look for inside, if anything?), and of course, their actual objectives.
Honestly, who wants to talk to some snot-nosed humans? They probably don't bother checking until the universe becomes one giant superorganism anyways. And even then maybe they just make their observations and ignore it as it tries to wave them down.
Alternatively - the spatial scales are very different and an entire galaxy or ours is not observable by their 'naked' eyes.