I THINK this occurs if you have the node selected when casting the spell. Not 100% sure but current game 0 probs making sure nothing is selected.
Tried this on a differant shard (an air shard), made sure I did not have it selected. Cast the corrupt on it..another useless death shard that I can't build, but in this case, the original air shard is in fact gone, and only the unbuildable death shard is on the tile. I did have that shard built before I corrupted it, so not sure if that is part of the problem or not. I'll try another if I can get an unclaimed, unbuilt shard in to my territory.
EDIT: Found another shard, that had not been built on. Built an outpost next to it. Made sure it was not selected, and cast corrupt on it. I was able to build the death shard.
Seems 2 things apply. Corrupt doesn't work correctly on an already built shard. Corrupt may not work correctly if you have the node selected when you cast corrupt.