Is she complaining of pain/discomfort anywhere?

No, but she has not been riding much...

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2014 P3 DI2 - RT6, CXR80, Power2Max S, 820, Fenix 3 HR. (gone)

It could be a couple of things. Like you said, her cleats might be too far forward. How does she ride on the same bike with flat pedals? If she is toe down then, her seat is probably too high and she is compensating for it (or maybe the nose needs to be angled down ever so slightly to relieve soft tissue pressure). It could also just be that she is new. I have noticed a tendency of a lot of new riders to ride toe down. I suspect that it has to do with fitness because I have noticed the same thing when experienced riders get tired.