Use a sterile potting mix (typical for seedlings), and clean the new pot with a sanitizer like bleach. The fungus that causes "damping off" is ubiquitous in all non-sterile potting mix, garden soil, and native soil. There is almost always some % loss from seedlings due to damping-off, and there is a lot more going on then just the stem. You may notice several weeks of poor or stunted growth before the plant wilts or keels over. This is when the actual roots are infected before the fungus destroys the stem. Throw out the seedlings that have clearly stopped growing.

Two days since you got it? Your tree has really been whipped around a lot lately. Trucked to the store, maybe too wet or too dry, harsh sun it may not be used to, windblown at some point, transplant shock as Scott notes. It may be disease of some kind, but it also looks like mechanical damage from the above causes. I have an apple tree that acquires a very similar look each May or June on the north side after a howling wind. I would just keep an eye on the new growth that comes out and see if it continues. More than likely it won't.

Perhaps others can give you specific advice on how to winterize your tree, but here are some thoughts: Apple root balls get big. If you're planning to have this thing in a pot for a couple years before you move, you'll need a big pot eventually, no? Maybe moreso since the roots will be those of a standard apple (not sure on this point, though). Those I've known who keep fruit trees in pots usually have dwarf trees. A lot of people will say, "you can make any tree any size by pruning," but it seems to me you'll still have the vigorous roots to contend with. People keep all sorts of plants heeled in all winter long. I briefly considered heeling in some seedlings in the bed for the winter before planting them out next spring (I gave up this plan to encourage better root growth). Except for heeling them in, I wouldn't have winterized them in any way. In your climate, maybe things are different, but if I were you, I'd just leave them heeled in. Maybe consider trunk protection (hardware cloth or something) to keep the critters from munching on/girdling your tree under that foot of snow. I've never espaliered fruit trees. I wonder if it's easier/better with dwarf/semi-dwarf rootstock. My dad planted apple trees everywhere he lived and always said he was happy to leave them for future owners to enjoy when he moved. Maybe you just want to plant it and be done? Maybe graft on some edible fruit so that people are more inclined to keep it. :) Anyway, good luck!

soak for no more than one day ... get some media... moisten it .. and pot them up .. and put in full shade... and see what happens .. if you dont have all that laying around... just shove them in mother earth .... in a little nursery bed .. and if any of them wake up.. you can move them in fall ... sounds like you made a donation to arbor day ... your experience is extremely common ... nice place to make a donation ... but not if you want quality stock .. ken