The Marvel Cinematic Universe is really, really, really big and the movies it produces are put together by thousands of people over multiple years, with a constant eye on how it effects the entire arc of dozens of characters and future movies.
In short, editing them must be an absolute nightmare and if you've listened to any of the commentaries on the disks you'll know that huge amounts of material is trimmed and sliced and entirely reshot for pretty much every film.
The most recent entry Civil Was no different and you can get an idea of what dropped out in this new deleted scene.
It's a pretty small moment and it seems like this was dropped for pacing but it's also important enough as it shows the power of the Wakandan nation in a way that's not totally clear in the final film.
Still the pacing has to remain fast to keep audiences engaged and we can see why this might be cut if the running time was getting long. The full disk will be out on the 5th of September 2016 and will have even more deleted material plus an audio commentary, making of and a gag reel.