what surfaces do they have her running on? is the geology similar to where she grew up? i grew up playing home youth/HS soccer practices and games on soft, well-manicured fields that were a tad muddy. no joint issues. as an adult the league played all its games on a different complex which is part of a reservoir. very hard ground particularly in dry periods. i had sometimes had sore knees after playing road games there as a kid. i tore up my knee there in men's league as an adult after weeks of knee soreness during a drought.
i mean, to me, the 4 most obvious choices would be the surface at the college, what she eats there, how hard they work them, or some maturing body issue. either body change or the mileage is catching up to her cumulatively.
all due respect to the folks on here but different people handle mileage differently, and your body might handle even the same mileage pounding differently if the geology they ran on was harder than before. and if you're multisport some coaches make appropriate adjustments and some don't.