not sure if I've really got your point.
When swimming longer than 5-8min our bodies need to switch from anaerobic state into an aerobic state to go on for longer. (Same in byking or running, but there you can breathe a little more often and arhythmic and will not feel it as in swimming where your breathe has to be more integrated.) This switching often feels as some discomfort in breathing. You can get around or at least soften it, if you break your warm up into some smaller parts with a short rest intervall of 5-15sec (100m-300m pieces). Give it a try.