Was it just you? Or do they apply the same policy for every visitor with a bottle of liquid?

Just a guess but at a museum I assume they're looking out for vandals. If it's a water bottle the counterpart would be something like concentrated sodium hydroxide in which case a single sip is sufficient.

Not sure how they would handle dye in a paper coffee cup though.

This is/was fairly common, I've experienced it on the Chinese subway a few times and I've seen a few clips of it happening online. No idea if it's official policy or not, though.

I saw them do this to a few others in line.