No I haven't, to be honest. Have you considered it's your cleaning regime, not the bottles, that my be the cause. Some juices are real sods, when it comes to cleaning?
Soak in Bicarb, then wash in hot water with detergent. You can soak them in bicarb, again, then rinse if you wish. It's also worth pointing out some juices damage these silicone bottles, too.