They probably would have done one when it was brought in, but animals have to be anaesthetised to have tests like that done (they can't be told to lie very still the way humans can). Since anaesthesia comes with a risk of death just on its own (it does in humans too!), it's not something you do unless you have to. So yeah, when the animal was first brought in after the accident, they probably did do MRIs and/or X-rays because it would have been medically necessary. But they wouldn't have done them again later if the animal seemed to be recovering from its injuries, because they'd have risked killing it in the process. It's a very real possibility that there was some residual internal injury that wasn't obvious at the time it was injured, but which caused it to die a few months later.

Plus, yeah, it was an unusual hybrid, and there's no way of knowing how that affected its health. What happens with hybrids sometimes is, say, Species A has a gene that causes a health issue and a gene that fights the health issue. Species B has neither gene. So when Species A and Species B mate, the offspring can end up with a gene that causes the health issue, but no functioning copy of the gene that fights it. Thus, it gets the health issue and then dies. Sometimes this is obvious shortly after birth - it's not uncommon for hybrid animals to die within days or months of birth. But sometimes it's the kind of health issue that takes a year or two to cause a serious enough problem that the animal dies. Maybe with this animal the combination of genes it had affected how it healed from its wounds, leading to it dying of something a pure dog or pure fox would have recovered from.