Shoes are tricky - even when they feel a good fit in the shop, you can't replicate the pressures you put through them on the bike to be entirely sure. Then, once you have attached the cleat it's too late to take them back.
I've got pair of Giro road shoes that are very comfy off the bike. On the bike, they've been a bit hit and miss - sometimes they fit like a (foot)glove, others they're not quite right. I've tweaked the cleats, but I think I've narrowed the issue down to how I fasten them up - my foot needs to be as far back in the shoe as possible when I tighten them.
What they haven't had is a really good soaking, which from past experience helps deform and reform shoes to your foot. However, as they are my summer cycling shoes it won't be long before they receive one of those...