To replicate: with an empty bucket, move your cursor quickly between two blocks of water and right click as close to the intersection as possible.

I did this several times by accident before I suspected it may be a glitch and started being able to do it consistently on purpose. The water pictured below would stay in this state until I interacted with it again.
Most of the time after doing this trick I would have an empty bucket. The pic below is an exception where I think I accidentally scrolled to another bucket in my inventory.

Because I was able to fill a bucket with this empty space, I suspect the game thinks that it's still water, but isn't rendering it properly. didn't think to try swimming in it or further poking. Figured I'd leave that to the pros!