I bought a bad load of fuel years ago that probably had a lot of water in it. Chub Cay had been out of diesel for a week, leaving me marooned there. (Note: ALWAYS have alternate fuel sources available in the Islands.) The tanker arrived at night. Next day I filled up. I should have allowed a day for the fuel to settle and the water to separate. Back to the USA, again filled tanks, then stored boat for maybe 9 months. Bad fuel contamination. Since then have added Biobor before storage. Have had no similar problems since. Half of the small bottle goes in each tank before I fill. I think Racor makes their own brand of Biobor but it takes a lot more of it to treat my 586 gallons of diesel and is more expensive.
I do get dirt like that in my Racors. I don't know what it is but I suspect a precipitate such as asphaltene coming directly from the fuel. Or could just be dirt. The filters seem to catch it. We did about 800 nmi this year, about half over open ocean swells and the filter vacuum gauge never even budged. I clean the bowls as they need it, but usually once a season does the job. I seldom see more that a teaspoon of water in the bowl. If there's more I know something is wrong. Caught my leaking fuel cooler that way although it took me a while to figure it out.
Be sure to change the O-rings in the fuel and water fills every couple years. They are in a demanding environment. Unlike most marine items they are pretty cheap.