That's a real problem. Dormant oil spray (often mineral oil and lime sulfur) is good to use only before the tree begins to leaf out, and I think you're too late.

Typically, bees are only around fruit trees during blossoming, but spraying into the atmosphere at other times can still affect bees which have to share the air.

I'm not too late here in PA. The buds are barely thinking about swelling on my trees. So I'm guessing if I can get some dormant oil spray ASAP I should be good to use it with bees on my property.
I was hoping there was some type of organic spray that will keep spots and that type of them in check and not be an insecticide.

No - pesticide residue remains, bees will avoid it but they'll still pick it up

best I can recommend is research "Peaceful Valley" and others that sell lacewings, praying mantis and ladybugs...

for fungus, mildew and those things I wash the plants and trees well with water from a hose then use straight baking
soda

start identifying single issues and finding the organic treatment for that one thing

dishsoap - is especially effective sprayed directly on bad bugs