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.

I've tried it again, this time paying more attention to the alerts. But I still can't reproduce it, the alert goes away when I acknowledge the chest (while inside the building), and when I leave the building, it stays that way (no alert).

Is it perhaps an alert for a different logistic chest that you haven't acknowledged? Or it's a problem with a different mod (although I don't know what could cause that). Oh, and which Factorio version are you on? 2.0 or the experimental 2.1?

If you want, feel free to send me your save file via mail (factorio@binarydiv.dev), then I can have a closer look for myself.

Currently on 2.0. I can check this on 2.1 as well. Thanks for your time in looking at this. I will see if I can gather more information.

I quit using 2.1 due to a bug that is randomly sorting my personal logic requests, disabling the Max setting value, and deleting additional personal logic tabs and combining everything into one. I need to look at that again and see if it is still happening.

Edit: I restarted my game in 2.0, and now the issue went away. I don't know what was different, other than adding a mod. earlyrissimo_1.0.1
Looks like this can be closed. Sorry for this. As you mentioned above, it must have been a different logistic chest that I did not acknowledge.

Ah, all right then! Don't worry about it :D