When you eat vegetables sprayed with anything, you are getting some small amount of residue. You'd better make sure that residue is safe before ingesting it. Most microorganisms found in your garden are harmless or beneficial. It's only when you try to create a sterile environment in your garden, that you create a place for harmful microorganisms to flourish. As an organic gardener who uses lots of compost, your plants should have a nice coating of harmless microorganisms on them.
Plant leaves only have so much space to support fungi, mold, bacteria.
If you innoculate your plants with harmless organisms from your compost, the bad ones from elsewhere can't get a foothold. Plus, the microorganisms are breaking down plant residue and making the nutrients available to your plants. Without these microorganisms to decompose organic matter, human life would be impossible. We should be celebrating these little buggers and not trying to eliminate them. Finally, some fungi and bacteria live with your plant roots and provide nutrients to them.