I have experienced this also, the way I "fixed" it was by having all supplies backpacks opened. And sometimes with ammunition it even says you looted them if you don't have the ammo backpack open.
But there should be another solution since that's not very good imo, u don't want to have all of your backpacks opened xD
Would be lovely if you could look into some other way to count items. An idea would also to make the HUD more adjustable (since it's the only public one i can find..) for example let us customize what we want the hud to show and the place of it. Maybe even integrate a Loot HUD? http://forums.xenobot.net/showthread...l=1#post469878 (like this)
Obviously you can edit it if you're experienced I have personally removed some things (like ping, session length, shadowHUD and all the big spaces) that I found unecessary but i'm sure ppl would love to have a config of what the hud should show.