Combine the butter and vanilla bean seeds in a small bowl. Fold in the pecans and season with salt and pepper. Cover and refrigerate for at least 30 minutes before serving.
Preheat the oven to 375 degrees F.
Place the Brussels sprouts in a medium roasting pan and toss with the oil and season with salt and pepper. Roast in the oven until lightly golden brown, 20 minutes.
Remove the pan from the oven, add the pomegranate molasses and stir to combine. Return to the oven and cook until just tender, about 10 minutes longer.
Transfer the sprouts to a large bowl, add the pomegranate seeds and lime and orange zests. Transfer to a platter and top with some of the Vanilla-Pecan butter.