If you thought that the internet could only be used for bad, then you wouldn’t have it either.
I’m assuming that you think it can be used for good as well as for bad things and you use it because it can be used for good and necessary things. I would also assume that the rebbe uses it only for good things.
I would further assume that you would have a positive outcome if you were to approach the rebbe respectfully, explaining that your son felt confused to see his rebbe check his smartphone during his learning time which he was taught should be sacred (even if it was during davening), and then to an the rebbe for his thoughts on it.