Is this a school band? As a band director, you should feel comfortable triaging each instrument yourself. Were I in this situation, I would go fetch my own soprano sax mouthpiece, take the instrument, and either verify it is working correctly or demonstrate the correct embouchure.
Those are really the only two possibilities: either there's a major mechanical flaw, or the player's embouchure is really poor. When you visually inspect the instrument, make sure you pay attention to the cork on the instrument neck (where the mouthpiece attaches), watching out for leaks; check the mouthpiece itself for chips or reed issues (perhaps have the player try a different mouthpiece and reed).
If the instrument is in tune above a certain note, and out of tune below; you should be able to isolate that note as the location on the instrument where there's a mechanical issue. Due to the way saxophones work, a problem at the bell end of the instrument is only going to affect one or two notes, while one at the mouthpiece end is going to affect all of them. A problem near the middle G key is going to affect the lower notes, but the ones above (until you reach the octave key) should be fine.
INCIDENTALLY: The octave key is one of the first places you should look for problems like this. Make sure you know how the octave key is supposed to work, and realize that there are actually two small pads in different locations that are actuated by the octave key based on whether the G key is pressed or not. One of these keys effects an interval of a 5th, so if that hole is clogged (it's very small), or the pad is not closing properly, it may be the source of your issue.
If everything is in full working order, then my guess is that the player is just not forming an embouchure correctly, and it is causing the instrument to be out of tune.