The symptoms pictured are probably caused by an environmental stressor (especially if it's in a container; temperature fluctuations are one possibility) and not an infection. It doesn't look like Apple Scab (a very common apple disease), though we can't rule out the disease Marssonina blotch. (It's still a bit early for those symptoms, though.) For now, just keep an eye on the plant to make sure symptoms don't change or worsen markedly. Leaf damage can't heal, so these discolored lesions won't go away even if the plant recovers, but as long as new growth looks better and the damage doesn't spread much, it probably won't be too impactful.

Fruit trees grown from seed will usually have different traits than their parents, so fruit quality, plant resistance to disease, final mature size, and other features that were known for the parent plant(s) will be pot-luck in a seedling. Apple trees tend to be grown on dwarfing rootstocks, for example, so seedling trees not being grafted will likely mature quite larger than those counterparts, so harvesting (once it ages enough to begin fruiting, which will also take longer since it's not grafted) and applying a pesticide treatment might be challenging several years from now when the canopy is large.

For now, it may help to familiarize yourself with typical apple ailments, if you aren't already aware of them, by browsing the Growing Apple and Pear Trees page linked above. For preventative pesticide applications (organic or otherwise), options are presented in the Virginia Tech Pest Management Guide publication, which you can search for "apple" to reach the applicable entries. Fungicides cannot cure existing infections, but they can help prevent severe outbreaks; insecticides should only be used once a pest ID is confirmed, though sometimes they too need to be applied preventatively since using a treatment after damage has occurred might ruin a year's crop.

Miri