For light infestations, hand rouging or spot spraying Roundup should provide noticeable benefits. In many cases, the infestation is too dense to make this a feasible approach. If mowing is done after thistles have produced viable seed, be sure and spend a few minutes cleaning the mower or chopper before using this equipment in thistle-free areas. This will prevent the inadvertent introduction of thistle seed into areas not presently infested. We continue to get questions about plumeless and musk thistle in established alfalfa.
Some fields seem to have surprisingly uniform stands.
Some move in with the wind, others perhaps with manure. It is hard to imagine that harvesting alfalfa 3 or 4 times a season allowed thistles to set seed. There are no confirmed effective herbicide treatments to kill biennial thistles in established hay fields. So if the problem persists, rotating to corn for a year or two is in order.