Protein skimmers are excellent devices to do so. The skimmer is actually undersized for the type of tank you have The animal load is higher than the protein skimmer can handle The skimmer is not operating at maximum efficiency. All the above are examples of a certain amount of organic material being removed, but the amount removed is smaller than the amount produced. The net result is that the amount of D.O.C. rises. Let it rise for long enough and undesirable algae will appear, guaranteed.
Organic material is made up of protein.
Protein breaks down into many organic compounds, some of which are obvious and some of which are not. Amino acids make up protein and are an example of the former. Complex organic compounds that break down when protein disintegrates are examples of the lesser obvious ones. What has happened here is that over a period of time, due to problems related with the skimmer or any of the other reasons mentioned, the amount of such organic compound has slowly, but surely, increased. This may also explain why it is not uncommon to see more of them in the summer than in the winter.