What do you mean?Logical Problem:
The Ship Shelter produces neither Minerals nor Unity. So you get a "Supress warning", even though the next upgrade and all the ones after do produce that 2nd resource.
It is less of a issues with unity, as presumably only buildings produce it (no tile yields).
The Ship Shelter produces Energy & Unity right from the start. The suppress warning is still valid if you're trying to place it over a food and/or minerals tile instead of an energy tile.