Another common cause of bubbly bottle-fills is missing the flow sweet spot on the spigot.
You can turn the valve 180 degrees to start the flow of beer, but if you turn it too far or not quite far enough, you get a torquing, twisting stream that agitates/aerates the beer as the bottle fills.
It took me longer than I'd like to admit to figure out that small changes in the spigot valve setting can have a big impact on the turbulence of the beer stream as it feeds through the bottling wand.