I have an old quilt that did that as well (it's actually hanging on my chair behind me right now). I did everything I could do to it to get the stains out, but while they lightened a bit, they definitely remained. As it is a white quilt, they're very noticeable.
As far as I can tell, they're just age/fold lines. As long as the rest of the fabric, when used in a quilt, is not sitting folded forever, should be fine. I really don't understand WHY these things happen, I only recognize the circumstances in which they happen - in this case sitting, folded, for a long period, will often result in yellowing/discoloration on the fold lines.