Cellular Malfunctions?

Also add the formation of proteins that don't work efficiently or effectively to the list. I'm thinking of cystic fibrosis in humans. A mutation in a single gene causes the body to produce thick, sticky mucus that clogs the lungs and blocks ducts in digestive organs. Ultimately, the aftermath depends on whether the mutation arises in a somatic cell or a germ-line cell. Mutations that occur in somatic cells usually remain silent, and are dissolved away via apoptosis. They may remain as silent changes contributing to organism diversity, but may also be dangerous in the case of cancer.

I mean more that the damaged cells themselves become issues on the micro scale than organ issues of specific nature.

One cell can't do much harm on its own. Unless, however, it replicates via mitosis and the mutation spreads to surrounding tissues. This then leads to the cytological issues that's characteristic of a disease - depending on where the mutation occurs. But a single cell impacted by mutation won't do any harm to the organism most of the time