I've only seen this issue one time so far. Plains hex, showed items on the ground on the hex map. Clicked the items button and nothing is actually on the ground. Screenshots: http://i.imgur.com/1v5qR.png and http://i.imgur.com/enHSm.png
Yeah, I've been getting that sometimes too. I've been assuming they're items that only show up when you have a specific skill and so you can't find them when you arrive at the hex.