The US and Israel never had the right to attack Iran in the first place
Claiming that a country can't exercise military control over its territorial waters seems like a legal or political fiction to me. Granted they share part of the waterway with their neighbors but expecting a country at war to honor such things also seems like wild fantasy to me. They've been bombing those same neighbors.
Of course in the real world law takes a back seat to force.
> their territorial waters extend only 3 NM from their shores
Do you suppose their current government would agree with that statement? Personally I rather doubt they would.
But even if they did, as you say law often takes a back seat to force in these matters meaning that they could just as well say "yeah you're right but we're at war so get bent".