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It will phrase match if the stop word is in the middle of a phrase it matches. If you get the message "common word", then the word isn't in the search.
I hope I can get further clarification. Let me give a tangible (but fake, I have no affiliation with Tampa hotels :) ) example.
Search for the following
1) hotels tampa // gives a set of results
2) hotels in tampa // gives a completely different set of results
3) hotels on tampa // gives the same as #2
4) hotels at tampa // gives the same as #2
5) hotels by tampa // gives the same as #2
So here is my question.
First of all, the stop words clearly have some effect (as Brett said), or the results would all be identical to #1. So, if they do have an effect, how do the searches 2-5 all provide the exact same result? I would anticipate that if the stop words are included, that there would be some minor fluctuation in the searches 2-5. Is it just sheer coincidence that all of these pages are equally optimized for "hotels in tampa" and "hotels at tampa"?
I think my confusion may be the result of not properly understanding what "phrase match" means.