I've had this question for several months now, and haven't been able to find a satisfactory answer online.
The Japanese し and the Mandarin "xi", as in 西, are listed equivalently as [ɕ] in the IPA.
However, my girlfriend and I can fairly clearly tell the difference between these two sounds, even after trying to isolate the consonant in the above words. (She is a native Japanese speaker learning Mandarin, and I am the opposite.)
Are we imagining things, or is there actually a slight difference in [ɕ] between languages? If the latter, are they marked as identical in the IPA because no single language differentiates between the Mandarin [ɕ] and the Japanese [ɕ]?