i don't think it has anything to do with Connecting Threads quality of fabrics- if it was a layer cake it should contain fabrics from all the same collection- which means the fabric (should) be all the same quality---
unfortunately sometimes something seems to go wrong in the manufacturing process.
i think you should send an email to Connecting Threads describing the problem...
they may have advice- they may even replace the layer cake- (if its a line still available) you never know- but it's worth it to let them know this happened.