If the horse isn’t getting clean changes consistently, he isn’t fit enough to be working on changes or he has a soundness issue that makes the clean change difficult.
I’d stop working on changes for now (do simple changes instead) work on fitness and really developing a clear three beat rhythm at the canter.
A late change behind or multiple strides of cross canter while on course in the hunter ring is usually scored as a major fault, though it’s at the judge’s discretion. It can knock your score down to 60 or lower.
You’re right in thinking that continuing to do this will make it a habit. Right now he’s saying that cross cantering or changing late behind is easier for him than a clean change, I would not continue reinforcing that.
Here’s a great exercise that may help:
After you ride a line or a single fence, come to a complete halt at the end of the ring. Pat the horse, and move him over a step or two, off your inside leg. Then pick up your canter and go to the next fence or line.
This teaches the horse that to expect a rebalancing prior to a turn or a change of direction, a very useful thing.
IME, if you do this consistently, one day your horse will offer the clean change before you ask for the halt/mini leg yield/canter.
If the horse has a late change in this scenario, I would bring him back to a halt, move off the inside leg, and canter again.