I have received reports from two independent sources, both using the steam version, that they lose items (ammunition, repair tools, and medkits were mentioned specifically) randomly (both in terms of frequency and quantity) during level transitions and the loading of a saved game.
I have not personally encountered this, and so cannot discount the possibility that they might simply have used the item and forgotten about it.
I don't want to add it as an issue without more reports, and definitely not without a fix or workaround in mind. Just wanted to let people know.