The logic chest inside the Factorissimo building is flagged as missing. It needs to stay that way to allow for multiple different things inside.
Going inside and setting the flag to ignore it does not work.
Maybe because inside the building, the player is on a different surface.
Can this be fixed?

Hi, thanks for the bug report!

I'm not entirely sure what you mean, though. I also haven't really played with Factorissimo in a while. Can you elaborate what you did, what happened and what you expected to happen?

What I've tried to reproduce it: Placed a Factorissimo building, went inside, placed some logistic chests. Without a filter, they show the warning icon (as expected). Using the acknowledge tool on them works just like outside (warning icon replaced with green icon). So I assume you probably mean something different? Or is this not working on your side for some reason?

Yes. I do get the acknowledge when going inside the building and I see the small green symbol. But when I go back to the main Nauvis surface, the errors on the bottom right of the screen do not go away. Also note that this was tested after all research for Factorissimo 3 was researched. I think it may have something to do with Nauvis is one surface, and inside the Factorissimo buildings is a different surface.