Editing size of library element is broken: modifying canevas size in CC library object changes the object's scale in existing documents
To replicate this, create a square with a fill and no stroke in a new document. Drag the square into the library panel to create a library element. Drag an instance of the library element you just created back into the document. You will have two identical squares, one which is just a plain square, the other which is a library element.
Edit the library element and make it a different height. Save the changes and go back to the document. The library element is now not the same width as the original square, although you didn't edit that. If you select the library element in the document, go to the properties panel, click on linked file and expand all info, you will see that it's scale has changed. It is no longer 100%.
If you add a new instance of the library element, it will be scaled 100%.
Simon Demeule commented
This is using Illustrator 22.1 on MacOS Sierra 10.12.6