Each drilling area has its own unique geology. Something about this specific area (e.g. heavier mud, cracks in the bed rock) led to their hole collapsing before they could reach their target depth despite trying a few different techniques.
All most likely true. And yet, the Nature article clearly states that the Chikyu set the record for deepest hole drilled. They don't qualify about unique geography or for-scientific-purposes. This is odd. I generally find that Nature tries to be accurate to a fault. Having written a "news and views" for Nature once, I find the seeming inaccuracies incomprehensible.
I pointed out above the Deepwater figure is depth from ocean surface while the Chikyu figure is depth below the ocean floor, so as long as the depth of the ocean is ~20,000 feet where the Chikyu drilled to that depth, it all checks out.