That's a very logical concern...and a good question!
Here's the deal: our bodies are NOT made of metal, they are porous...and hence whatever comes out of your liver & gallbladder are porous. If you drank a cup of beet juice instead of grapefruit juice when you flushed, everything that came out of your liver/gb would be mixed with the beet juice throughout your entire digestive tract for a half a day...and when you saw it in the toilet, whatever it was WOULD be red!
So, of course, the coloration of a 1/2 cup of heavy oil will absorb into porous debris.
The only thing that happened, is the stones look more yellow, because the oil they were riding along with for 1/2 a day (or longer) was yellow this time. If the oil had been blue, then they would have had a bluish tint.
Also to remember, bile is greenish/yellow (depending entirely upon what all, I don't know...but sometimes it can be more yellow, and sometimes more green - or so I've read). So I think it is very possible that our bile could affect the color of the stones, too.
And always remember, if lots of people weren't being healed and seeing marvelous results from Liver Flushing (no matter WHAT comes out or from where)...NO ONE would continue sucking down Epsom Salts cocktails, with olive oil/citrus chasers!