The warnings are not based off of facility type, but ability type instead. They should be more descriptive though.
If you have an Urban Pacification Center in the system and add a Medical Lab (organic races) to the queue, you get an error because they both use the system happiness abilities. But, building the Medical Lab is still worth building because of the other abilities. This is why the error message should tell you what overlapping abilities are present, but unfortunately doesn't.
Edit:
Wow, beat by a second with a post that quotes me. Oh, the irony.
Quote:
not necessarily the same effectiveness.
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I think that you do not get the error if you add a facility with a higher value for the ability. Build a Medical Lab. It gives 1% happiness. I do not think the game complains if you add an Urban Pacification Center II or III, because it gives a higher bonus. I may be wrong though, I haven't tested it in a while. 
[ March 25, 2003, 01:09: Message edited by: Imperator Fyron ]