", you've set up a sentence talking about something that happens habitually. It's hard to see how anyone would be able to interpret the sentence as a whole as talking about something habitual with regard to loudness, but a one-time event with regard to lateness. Even separating the two results in something anomalous: The train was frequently loud, and it was late.
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TheFisherTo resove all ambiguity, write the sentence as follows. The train was frequently both loud and late.
The train was frequently loud and late.