How big were your clowns when you got them? IMO anything under a 4' tank for clowns will stunt them fairly quickly, even at a small size when they appear "perfectly happy" in a smaller tank. Perhaps some of the ones you got had been sitting in the small tank at the shop for months but others had come in more recently? Genetics also plays a big part. We say clowns grow to 12", but that is like saying people grow to 6', when in reality that could be considered the usual but it can vary greatly.
I doubt the growth of the smaller fish is being suppressed by the dominant fish, biologically it doesn't make sense for a schooling fish, and the growth I've seen on the 10 or so smaller clowns I've been growing out from a small size in my group of 30 certainly indicates that it isn't the case. If you aren't feeding enough food then obviously the smaller clowns will suffer, but with proper feeding and water changes it shouldn't be a problem.