Hi,
As a swimmer i know the feeling! I would check for impingement of the Sub Acromial bursa and ask her to show you her freestyle stroke technique. see if she internally rotates and adducts at the hand entry into the water as this will impinge the bursa. I would suggest asking her to widen her hand entry slightly and flat hand entry rather than thumb down to see if that eases the discomfort during swimming. Also would be good to see her stroke in general as if she isn't getting enough body roll then the arm adducts and horizontally flexes during catch and pull which will also impinge the bursa.
Tests for impingement that are really quick and easy are Neer cans, and the Hawkins tests.
palpation during stroke replication should confirm if that is in fact the problem. NSAIDs for a few days and easing back into swimming with concentration on stroke rather than full on speed and distance should also help.

Let us know how you go!

msk101