My urban apple tree has yellow spots on the leaves and small holes in the leaves also. I have 2 urban apple trees that I planted in large containers (Golden Treat and Blushing Delight). The Golden Treat I have had longer and was larger when I bought it at a local nursery and has the yellow spots/holes on the leaves. The Blushing Delight I ordered online and seems to be doing ok.
Urban Apple Tree Has Yellow Spots on the Leaves
Certified GKH Gardening Expert
This could be an insect damage or even alternaria leaf fungus.
I would treat with something like Neem Oil. It works as both a fungicide and insecticide.
Here are some links with more information.