Yes, it might be pathogenic but your description is not nearly adequate to make a diagnosis.

Because of the timing and circumstances surrounding this planting, I'd be very hesitant to immediately assume it was some sort of disease issue. We are more likely looking at transplant shock and an early dormancy, which can often be triggered by planting late in the season. Excessive rainfall during this period could certainly account for what you describe as well. Retaining dried, dead foliage is pretty common for this selection also. As long as the container is filled with a high quality, fast draining potting soil and offers adequate drainage, I'd wait until spring to see how these trees bud out before I'd do any thing else. They will probably be just fine.

I was going to post this same thing I've got a full grown what I believe is a 'Bloodgood' Japanese Maple that has been red every year except this year. We had a lot MORE rain than usual this year so I assumed that was the cause of the green leaves but it hasn't rained in a while now and they never turned red. Perhaps the nutrients got washed out of the soil? It looks like we are ALL still in question on the why here so... RESEARCH TIME! This is the best information that I found: Japanese red Maple leaves turn from red to green when the intensity of light is decreased. Most if not all varieties of red leaf plants lose the red color if the leaves are in a shaded area. Our trees are grown close together to conserve water and help keep plants standing.This causes the new upper most leaves to become very red and the leaves that are shaded by other leaves to become green. Once these trees are given more space the red color comes back." (1) Here's another interesting point: "Trees grown from seed lose their red leaf color in summer, which may be disappointing to the homeowner. " (2) My tree is in a fairly shady side of the house and is full grown now so there will be no moving it for me... I do think that all of the overcast rainy weather did send it into the green state that it never got out of though. Hope this helped some of you! Here is a link that might be useful: Sooner Plant Farm

Maybe.....maybe not :-) There are nearly a thousand different kinds of Japanese maples in a very wide range of colors. But virtually all will go through 3 different seasonal colors - early spring leaf out, midseason color and fall color. There are many cultivars that start out in various shades of red in spring only to change to green during the growing season. And others do have red coloring that can fade or green out depending on how much sun or shade they receive. So we really need to know the cultivar name to be able to tell you what to expect.