In the all the apartments 99% of items spawn in the floors. I don't know if this is an environmental or item issue.

You can be directly over them but they most often will not show up as within the area on the tab screen. You can sometime kneel or prone on the floor then click the item to pickup. You know they are there because you can partially see the item if it's tall enough.

Some unseen items you have to tab screen and be prone/kneeling and you can get.