Bike computers include error from the zigzagging of the front wheel.
My suspicion is that smartphone GPS units use fewer channels to save power - my marine one tracks 24 satellites and picks the best for positional computation. Phone ones are hard to understand as the specs aren't published, but the iPhone 4s chip can track 12...whether it does is another matter. All get degraded by buildings and trees.
My marine one can accurately tell which side of the road you are on (not on a map, just using the track log).
In summary there are a shedload of errors. If yours is consistent then I would not worry. Remember that a 3% error on a bike computer is 2mm in diameter - so well within the range of tyre size and simple variation in inflation pressures.