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There are indeed some, although the vast majority of flies are normally diurnal. IIRC the tropics have more nocturnal species than the more temperate latititudes, including some in 'sun-loving' families such as Sarcophagidae.

Among the north European fauna, which I am more familiar with, nocturnal (or at least crepuscular - the summer nights here at 60 N. lat. are not really dark) species are found in here and there in many families, although there is next to no real research into the topic. Species like Ceromya silacea (Tachinidae) and Achalcus vaillanti (Dolichopodidae) are very rarely caught by netting during the day, but routinely caught with Malaise traps used exposed over several days. These two species are yellow, quite unlike close relatives which can be caught during the day.