Basically, everyone's feet (and walking style) are different. I discovered this when I started skiing last year; I got myself a cheap pair of boots when I started and absolutely hated it. After everyone told me I'd been an idiot -- that while you can cheap out on skis, pants, gloves, poles, whatever, and that boots are the only thing worth spending money on for beginners -- I went to a boot fitters and spent a few hours getting sized properly. Suddenly, skiing became one of my favourite pastimes.
Walking's similar. If you're walking in top of the line boots that don't fit your feet or your gait, you're going to end up injured pretty quickly. If you're walking in cheap boots, it's even worse. Find a shop with a wide variety of brands and decent staff who know how to fit you up properly (they'll often squeeze in orthotics to adapt for your gait too). Since doing that this summer, I've had a much more comfortable time hiking :).
This should not happened if you sized and laced them correctly.
Also, keeping your toenails short is an important thing to do.
There's always going to be wear and tear on your foot when you're out and about (and legs -- part of my problem is that the pair of shoes I had didn't adjust for the way I stand/walk, and now I've got ITB/knee problems), so there's no miracle cure. But a properly fitted pair of shoes goes a very long way :).
I do a lot of walking these days, and my foot health has improved dramatically. My toenails are also healthier and I have less edema in my feet and just a lot of changes.
There are other things that go when you hike a lot. But my guess would be that you have some kind of medical condition and blood-related in some way is the first thing that comes to mind.
For a couple of years, I hiked in shoes I thought of as really comfortable. On long walks (especially 35m+ in a day), I'd get blisters around my heel and sore toes. I just figured that was what happened when hiking a lot.
Changed shoes (same brand, but larger and better cushioning) and haven't had those problems since.
Also make sure to keep the nails trimmed!