When a player has an inventory open, and a plugin sets the player's armor, those pieces of armor appear in the top right slots of the inventory they have open. For example, if a player has a chest open, and I set their armor via setArmorContents() or setBoots(), setChestplate(), etc. that armor appears in the chest.
I am pretty sure the items are not actually there, as they do not drop when a player tries to drop them, and they also disappear when the player logs out and logs back in.
I have attached a screenshot of this to this issue report. Here is the code I'm using that caused what you can see in the screenshot: http://pastebin.com/7D7v1sP7. This code is setting the player's armor (boots) every second from a random array of colored leather boots. The line that sets the player's chestplate to a diamond chestplate was added for debug purposes.
I should also note that this glitch does not appear in 1.8.3 or 1.8.4.
Thanks for your help.