I had a specific reason for suggesting you question whether your boot fitter is optimal:
Hagland's Deformities are, as far as I have been able to read about on the Internet, often or usually caused by shoes or boots that fit imperfectly (e.g., too tightly) at the back of the foot. Likewise bunions are also often or usually caused by fit problems, specifically too much pressure at the sides of the toes, especially the big toe. That
could possibly mean your fitter did one or more of the following:
1. They fit you for boots that don't match her feet very well.
2. They didn't do a heat mold, or did it wrong.
3. They didn't make other modifications to her boots that might have solved the problem, such as stretching out tight spots, or filling in loose spots.
As difficult as this is to believe there really are relatively few (probably less than a dozen) skate technicians in the entire world who are regarded by the figure skating community as being overwhelmingly better at such things than the rest. They don't tend to be the cheapest, and people often do travel long distances to consult with them. I watched one work for a couple months, trying to learn things from him. He worked in Maryland (but has retired

) but was often seen in person by people from far away places like Japan and Europe. And some of those people even regularly mailed their boots or blades back to him to get them sharpened. (Many of them had two pairs of boots or blades, so they could keep practicing while the boots were in the mail. Also so that if a boot or blade developed a sudden problem, or got lost in transit, they had an extra pair. Though since your daughter does both freestyle and ice dance, she would need 4 pair to do this - assuming she used boots that were separately optimized for freestyle and dance. Not all that cheap. But neither is seeing a distant podiatrist several times every time she gets new boots, or current ones develop fit problems.)
By the way, be sure to make an appointment to see whoever you see: don't just come to the store and assume they can see you. And come back when the boots arrive, so they can make final adjustments. And if a problem arises later, go back again. It's very inconvenient, and somewhat expensive but it seems like people who do this do tend to get better results - and maybe fewer long term health problems too.
Of course, I hope you went back to your fitter, and asked them whether they could do anything to solve those problems. If you didn't, then maybe you didn't give them a proper chance - without feedback, no or few fitters can always do an optimal job. Just like with doctors and orthotists. In all those cases, there are some elements of guesswork, and it is apparently hard to always get things right the first time.
Poor boot fit often reduces boot lifetime, especially but not soley for lightweight boots. I used to think that good, well fit figure skates should last for years, especially if they were sewn (rather than glued) together. But other more experienced people, like Ic3Rabbit, have indicated that it isn't unusual at this point in time for them only to last a few months of intensive use - Ic3Rabbit often mentions 3 months as typical here. If your daughter is doing both double jumps and ice dance, it is possible she is giving them a lot of use - more than many casual recreational skaters would give them in a few years. Also, between the fact that many boot manufacturers are emphasizing reducing weight, e.g., by using various plastics instead of thick heavy leather (which can be a fairly durable material), and cutting manufacturing costs by selecting glues that have desirable properties in the very short term, instead of sewing the entire boot together well, it is conceivable that modern boots are often less durable than older models. So perhaps only lasting 3 or 4 months doesn't
necessarily mean something is wrong.