I've also bought seconds, some are better than others. I have no direct experience with Marshal's or how they grade things. With muslin I'd look for "slubs" (the big bits of thread), sometimes you get one of those huge Frankenstein seams of two pieces of fabric, other times there may be some sort of damage from all sorts of things, water staining or grease for example. In print fabrics sometimes the print registrations are off or one is missing or something that may or may not be very noticeable. Sometimes that goes through the entire bolt, other times it's just a portion of the yardage.
Sometimes I have never been able to figure what the problem was...
A recent piece I got at the thrift store has some sort of black ink flecks on the off-white tone-on-tone fabric. Not a lot, no pattern I can discern. Since I know they are in there I can cut around them but would not be happy using large pieces.