A tad difficult to see details. But the brown areas look like a combination of superficial feeding (a long time ago) plus a shortage of water, probably brief and some while ago. In either instance, it's too late to do anything. For the critters, just keep a watch next year and squish when you see them. That said, the amount of critter damage in the images is insignificant for the tree's health.

Thanks everyone for the replies. @ken_adrian that is the thing that had me alarmed this particular apple tree usually does not shed its leaves until around mid-September. So I knew there was something wrong with it. After some consideration I think the brown spots was my doing :/ I tried to spray the tree with some "natural" bug killer since there was an unusual amount of wasps circling it, and I think I might have sprayed a little too much. @i_like_pi it does look like it has Cedar Apple Rust. The neighbors have a crab apple tree in the back, and it looks like that tree has the same growths. So I think that tree might have passed the cedar rust on to mine. I plucked off all of the leaves with the growths and so far I have not seen any more growths pop up. So I think I caught it in time. Once again thanks for the help.

I just don't ever experience hail damage so can neither confirm or deny......although it seems very strange to me that hail damage would appear along the trunk or the underside (or close to it) of any branches. IMO, it looks more like the beginning of apple anthracnose. But I'd suggest taking these photos and any samples you could manage to your county extension office for both an accurate ID as well as suitable treatment options.

Oh, what fun! Sorry for the delay, the last couple days have been busy (for many of us, I'm sure!) Dry out the soil a bit now that you're past the initial sprouting phase. It looks like you have the beginnings of a fungal problem there, and I don't like the way the base of that sprout looks. I'd separate it from the healthy one for now as well until the issue resolves itself...or not. Damp-off is a common issue with younger "trees" until there's more development. Very young apple trees are difficult and you're now heading into the most difficult season (source: my cousins own an apple orchard) and you started those seeds at the wrong time. That's OK, we can work with it. I'm going to agree and disagree with some of the above. If you're growing these just for fun, great. Carry on. Or if you purchased seeds that will produce edible apples, also great. Although please note that "edible apples" is a comparatively relative statement. Without a lot of comparatively nasty chemistry, apples usually won't be very attractive or nice, or particularly good. And a great deal of careful cultivation (such as trimming branches manually back to usually 2 apples) goes into it, although it depends on the cultivar. Plus having trees of the appropriate age. And so on. You can do the research on that. There's the warnings on what to grow and why. Apples are not for the timid, but they're not as bad as peaches (the cousins raise those as well). Your window light levels won't be enough for those this winter. But putting a good LED light on them for an additional 10 hours a day or so will be. And you don't dare let those go dormant this winter. They're far too young, they haven't developed enough, and they're unlikely to survive the situation. It's also completely untrue that many deciduous trees require dormancy; they do not, although those who are not native to deciduous trees' areas and don't know apple trees or the like may not know that just due to ignorance. I've kept everything from deciduous hibiscus to crepe myrtle to an oak tree up over the winter. No harm, no foul. Just keep light levels and warmth up. They'll go partially dormant on their own, then drop leaf shortly before spring hits and rapidly re-grown new ones. "Dormancy" lasts about fifteen minutes. Some may require it, hence the "many" above, but I have yet to find it, and yet to find the sapling or sprout that demands dormancy at that age. Don't try it. Secondary source: turning my head and looking at the extended season ageratum, 3 deciduous hibiscus, desert rose (which really does prefer dormancy and I'm disallowing it on this one--but it is not a temperate-zone plant), a random mustard plant, and the 9 other things in 4 rooms. We can go into why it's not a wonderful idea to store dormant trees in sharply reduced light or complete darkness all winter (as my garage has no windows and many of the ones I'm familiar with don't), but that's a story for another day. Feed very, very gently during the winter, by which I mean quarter rate or less. They won't want much. When spring arrives--and I mean post-frost as the leaves won't tolerate a frost--adjust them slowly to sunlight as the window is screening out most ultraviolet. Start at an hour a day for 3 days, then 2-3 hours a day, then leave them out all morning, then after a week, they should be good for all day long. When ready to plant outside, place them in full sun, with well-draining soil, and feed well until maturity. Once mature, the tree will not want to be overfed, and follow instructions for proper feeding to produce fruit (soil test; keep good levels of potassium in the soil, and don't mindlessly toss potassium on the plant).