Could we have a list of mutually exclusive tags, similar to the synonyms list?
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The problem with "smart" features such as this one is the fact that we often can't foresee the situations in which this perfectly reasonable solution actually is a problem.
Take the word-filter for titles for example. Yes, the word "Problem" is terribly vague for a title and should most likely not be there. But as soon as you implement the filter, you'll find situations where the word "problem" is perfectly reasonable. And not only that, those who actually want to use the word seem to feel no hesitation to use such creative options as "problam".
While the latter might not happen all that quickly for tags (tag creation requires some rep after all), the former might. I personally see more value in just manually retagging problematic tag combinations where you stumble upon them. And perhaps leave a comment or a descriptive edit message.
I can understand your frustration, but I think that the feature you propose will ultimately end up being more of an annoyance than it's worth.