I was preparing an area of a river for some water wheels. To do so, one designates the surface of the stream for channeling out, and the miner stands on the stream and does so. The channel immediately fills in with water, and all is well.
Today, however, my channeling instructions accidentally caused the dwarf to channel out all the tiles around one tile (which would normally cause the tile to become a 'collapse'), but the tiles below being water meant that the tile was indeed unsupported, thus a collapse indeed occured!
At first I thought that all fine and dandy. Then I noticed that the area not only was not filling with water, but was draining. Occasionally, the tile over which the collapse occurred even showed itself dry (the little infinity symbol that is streambed). Basically, even though there is nothing below the steam (no construction, just solid rock all the way down. No aquifer, either, in case it is asked.), that specific tile now was capable of being an infinite 2-D well into which the river flowed eternally.
This is SO blatantly obviously a bug.
I fixed the problem in-game (though the bug still exists out-of-game), by using a canal and floodgates to drain the river upstream into a chasm, followed by allowing the bed to dry out (or go down to 1's and 2's), and covering over the problematic stream-bed tile (It still is a stream bed tile. Not open space. Stream bed.) with a stone floor. Immediately the ambient 1's and 2's of water were able to wash over it without disappearing, letting me know that the problem was solved.
Using version 40d17. Some modifications, but it's all superficial, like added plants and rocks and a gem and some smelter rxns. Stuff that would not, could not, be the cause of something like this.