It's possible that it could use a bit more time. S-04 can take a REALLY long time to bottle condition, so there's a chance that more time could give you more carbonation. I'd give it a couple more weeks to see what happens. The bottle that gushed, as @flars mentioned, could have a bottle infection or could have more suspended particles, which would increase the perceived carbonation. But if it does turn out that the priming sugar wasn't fully mixed, you can open individual bottles, prime them, and re-cap. But don't do this until you're absolutely sure that this is the problem. Double priming bottles is a bad thing.
I don't rely on the swirling of the beer while racking to mix the priming sugar. It sometimes works, but it always works if you stir it gently. My standard procedure is to rack to the bottling bucket, place the cover on loosely, measure the priming sugar for the actual volume of beer you have in a 2-cup glass measuring cup (after taring the scale for the weight of the measuring cup), top up to 2 cups water appropriate for brewing, mix it for a couple minutes to get the sugar mostly dissolved, and zap it in the microwave until it just boils briefly.
Once this is done, take a sanitized ladle and submerge the bowl of the ladle so the rim is JUST ABOVE the surface of the beer, but is otherwise empty. Pour the hot priming sugar gently into the bowl of the ladle carefully and slowly so it doesn't splash, and then slowly stir with the ladle in an up-and-down motion to get the beer moving around a bit, but not enough to splash or introduce too much oxygen. Some people stir every dozen bottles or so, but I haven't found it to be necessary.