Ah, I see where the confusion might be coming from! The BF tells the node which pieces to hold. By excluding expired pieces from the BF generation, expired pieces won’t be added to the BF. This results your node wanting to delete these expired pieces. But as the TTL process already removed the files, GC now gives a warning that the file cannot be found. This just means the TTL process was quicker to delete the file than GC, which is a good thing.
As @arrogantrabbit mentioned (and @BrightSilence mentioned for warnings when the opposite happens), these should really be INFO messages instead of WARNING ones. So no need to worry—your node’s just getting a little ahead of itself. 