mmr, shapes and text on the MouseOff layer will always appear. Ditto for those on the MouseOver layer, even if the layer is hidden, until they have a link, usually a button but could be anything that has over 50% of an overlap with a shape on the MouseOff layer.
Shapes and text on higher layers will always appear unless hidden in the Page & Layer gallery or are linked to from an object on any layer.
Shapes and text on the Page background or the Pasteboard background layers always appear but will be covered by any shapes above them on other layers. Also, such placed shapes do not retain links.

For your missing green rectangle, check it doesn't sit in its own layer and links itself to the same layer.
Personally, I would just unlink the Text Inside and see if things re-appear.

Acorn