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There's a double battle on Sea Mauville, with couple Lois and Hal. If you beat them, there's a 5% chance or something that they'll give you the Destiny Knot. Easiest way is to save before you battle them, then beat them and just reset until they give it to you :)
You can also get Destiny Knot by winning Master Rank competitions. There are 5 people that give you gifts after the competition and sometimes one of them will give you a Destiny Knot.