My rule is that if I'm making anything that there's a possibility that it will have to be washed in the future, then I always prewash and dry in the drier. If it's charms I wash them in the sink with fairly hot water and soap and let the darker ones soak for a while to make sure they won't bleed. But I wash every square, even the lighter-colored ones. Then I dry them in a mesh bag in the drier.
They do come out crinkly and messy and must be ironed, but when I do it this way I can be pretty sure I won't get any surprises re shrinkage or bleeding.
I for one don't think it's too surprising if fabrics by a certain manufacturer, Moda for example, shrink and bleed differently. They all contain different dye and often probably are printed on slightly different fabrics with different shrinkage potential. That's my take on it anyway.