The TSA is something that shouldn't exist in its current form. They very often fail their audit checks and normalize invading your privacy to an extreme degree like body scanners and pat downs. If water bottles are considered potentially explosive then why dump them on a bin next to a line of people where they can go off? This is low grade security theater that inconveniences passengers at best.
A friend has been challenged when trying to bring a nordic cheese (from Norway to France). The TSA equivalent said that it could be liquid if hot enough. Yeah... glasses too.
I believe the rule limits the actual container size if it contains liquid. Even if you have a nearly empty water bottle or are nursing the last dregs of a full size tube of toothpaste, it gets dumped or thrown out. So technically, if any water has melted at all, it counts.