Reference Point moves on objects when one object on page is rotated. Indesign 2019 (14.0.1) If one (or more) objects on a page is rotated, then the reference point on other objects on the page changes as you select through the different objects. This applies to text, picture, and tint boxes. If you try and make the reference point the same on all objects on a page, say the upper left point, then select other objects, they have changed to a different reference point. This makes it very difficult to align objects from page to page.
Mac OS 10.12.6
What is happening is that after you have rotated the object by 90°, you have again chosen the reference point to be Top-Left. But after rotation, the top-right corner of the original (non-rotated) rectangle became the top-left of the rotated rectangle. That's why all other objects now show the top-right corner reference point as selected.
It has been like this since the very beginning of InDesign.
Adobe InDesign team