Would you recommend I try removing the stone dust from the joints to see if that helps? Scrape it out to be level with the bottom of the stone?

If my guess is right, then I think scraping out the "grout" between the stones would only allow water to accumulate in the remaining space (assuming it can't drain freely through the compacted stone dust beneath) which may actually increase the wicking problem. I would begin by doubling back with your contractor on this, to find out what they did and why they did it that way. My concern is that even with better drainage beneath the stones (e.g. coarse sand), using stone dust as grout neither seals the edges of the bluestone to repel water off the surface (as grout between bathroom tiles does) nor allows water to drain through freely. Unfortunately, the best solution would be to pour a concrete pad, mortar the bluestone to the pad, then use true grout between the stones. Otherwise, if you do keep an aggregate base (e.g. sand), you would want the stones to be as tight together as possible, with nothing between them that would hold any water.

Hello to all, i seem to be in the same boat with my new bluestone installation

The nig difference is that my installation was put over a slab of concrete put down 20 years ago and covered with bricks. Bricks were removed, slab was is very good shape and bluestone was instated on about 1” to 1 1/2” of cement dry mix motar. Joints filled with water proof cement. After washing down the finiished patio a few days later the exact type of wicking occured on many of the bluestones and we are all baffled.

HELP! It's 2025 and I have the same problem. Did anyone figure out what to do? I have a brand new thermal bluestone patio which has dark staining around the perimeter of the slabs. Gravel and cement pad beneath it, and probably bedrock under that. Cement mortar.

As Verdance originally said, water is getting under the stone and has no where to drain to.