The fillet tool is designed for single tracks and does not consider differential pairs specially. That said, it should be no problem to fillet differential pairs if you account for this when determining what radius to use. In order to get a constant gap between the pair members through a corner, the radius of the inside track must be smaller than the radius of the outside track. In other words, both arcs must share a common center point. If you increase the fillet radius by the distance between the track centerlines (i.e. the DP gap plus the DP trace width) for the outside track, you should get a perfect result.
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