Well, with areas such as the feet, there's just a lot of parts, and sometimes the way they overlap can hide or obscure something.
The resolution of an MRI depends on the field strength, and the "open" machines are weaker than the closed ones. 0.6 T is a weak machine, 1.2 T is fairly strong, and 1.5 T or 2 T is very strong. (I'm such a geek when it comes to medical imaging technology, seriously)
But the most common reason for an MRI to miss something is incorrect reading. Happens all the time, especially when the person doing the reading has never actually met the patient and has only the most general idea of what her symptoms are. I've had it twice, once with ankle MRI that missed synovitis, once with knee x-ray that missed a small fracture.