Some extensions/gadgets/userscripts place icons in the .mw-indicators element which will create a floating box when clicked, placing the new box inside the indicator icon's parent element, using absolute positioning to place the box underneath the icon. (For example, in the Schema namespace on Meta-Wiki, the EventLogging extension adds such an icon with associated popout box.)

Recently-ish, a change in z-index values have resulted in the created box being placed "underneath" (as in, with lower z-index and thus hidden by) the contents of the #bodyContent element. This is due to the .mw-indicators element (which also has the mw-body-content class, shared with the #bodyContent itself) being affected by two CSS rules, with equal specificity: The .mw-indicators selector itself is set to z-index: 1, but the .mw-body-content { z-index: 0; } rule overrides it, thus placing it effectively lower in the z-index order (both have z-index: 0 and the tie is broken by document tree ordering), resulting in the hidden content.

Both rules are in the skins.vector.styles.legacy module.