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.
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.