We can assume that, as it follows citizens from the twelve colonies of humanity who haven't lived on Earth, (despite bearing striking similarities to us in other ways) the word "frak" is their own version of our similar profanity, "f**k".
It is also derived from the original Battlestar Galactica, where the word "frack" was used as a substitute for "darn" or "s**t, mostly to comply with broadcast decency standards at the time.
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"Frak" is used in Battlestar Galactica as a replacement for the expletive "fuck." It was created as a way to bypass network censors while still conveying strong emotion or emphasis. The term became popular among fans of the show and is now closely associated with the series.