I inherited two apple trees and a cherry tree on the property I bought 5 years ago near Owen Sound in Ontario. They are about 7 years old now. One of the apple trees is a hybrid of three kinds. I don’t like to use pesticides but the yellow apples especially, are spotty and deformed. One branch touches the ground and I will cut that off before it gets leaves in the spring. What can I do to help these poor trees in an organic way.
Presumably what you are referring to is your specimen being a fruit cocktail tree consisting of different varieties grafted together. And not it being a single kind with 3 different others in its genetic background. The practical significance of this first condition is typically each involved variety occupies a single section of the "cocktail". Maybe one branch only when the tree is still young and small. With the varieties being chosen by the grower for cross compatibility. So that if you cut off the one low branch entirely you may end up removing all or most of one the participants in the cross pollination. This depends entirely on how much you are planning to remove and where each variety is on the tree. Regarding the marking of the fruits shown the first picture may be apple scab. With the others perhaps showing other problem(s). Such apple maggot for instance - inquire locally about what is present in your region. And what to do about them.
For eastern North American apple disease information, try inquiring at https://growingfruit.org/. It's a US site with many experienced professional orchardist members who can be very helpful. It includes members from Canada as well.