I mean the game clearly knows - make it clear to the player.
Sorry to disappoint you, but there are many cases where the game also doesn't "clearly" know.
There are many types of rules and some of them are so generic that they cannot be checked "individually" (for the lack of a better word).
For example all the business with required/forbidden/provided services.
In this case, the game would (temporarily) remove the facility from the base and then calculate the global impact of all remaining facilities on the base as such.
The game will know that "the base as a whole has a problem", but it will not know "which facility or facilities caused the problem" or sometimes even what particular kind of problem it is.
So the game could only tell you that "there is something wrong with the base after removing this facility"... which doesn't tell you more than "facility is in use".
That's the price to pay for having ultra-generic rules.
Now, I'm not saying all rules are as complicated as this... we could indeed improve the error messages for
some of the rules... just saying we cannot do that for every single possible scenario/combination.