I had some red fabric to do that when I was making some wall hangings and rug mugs for Christmas a couple years ago. This happened when I was pressing the squares. I couldn't for the life of me figure it out at first, then I measured the square before I sewed it with another one the same size and measured it again after pressing, tried just pressing the red alone with measuring before after pressing, sure enough it was the red from pressing it. I was sick, because I couldn't find another red in town. A dear friend was coming in from near Dallas and stopped at Abilene and picked up some more fabric for me. I have never purchased that brand of fabric since. I also had this to happen with some gingham fabric I was using in a quilt. I think part of the reason was because the gingham is much thinner fab. than in past years.
If you are unhappy with it now, you will be forever, so take it out and start over to be happy my friend.