I see a strange behavior of Acrobat Reader/DC Pro here.

I use a JavaScript button to toggle the visibility of a (comments) layer in diverse documents. In some, but not all documents, there is the phenomenon that once I set the visibility of the comments layer to invisible using this JavaScript button, and then change the zoom factor of the PDF document, the invisible layer turns visible again.

The hidden layer even becomes visible if the document is only scrolled.

See the attached sample document that shows this phenomenon.

It is even stranger that this problem disappears once the visibility of the comments layer is changed one single time using the Layers Pane and the eye symbol. The issue then completely disappears, but only until the document is closed and reopened.

It also does not happen with all documents that have a comments layer and a layer visibility toggle JavaScript button, only with some documents.

See the JavaScript Toggle button on page 1 or page 3 top right.