Our pigs do the same. They have two drinkers, a Mexican hat that’s too heavy to tip over and a lighter weight one that they often tip over. Consequently the former is always muddy and the latter less so. They drink happily from both and don’t seem to come to any harm.
They eat a certain amount of soil anyway, so a bit in their water shouldn’t be a problem. If the water stood for a long time and got stale, that could maybe be more of an issue. Ours need both drinkers refilling twice a day every day, and three times in hot weather, so no time for bugs to multiply.