I couldn't find the cause for it. I originally thought you can't pick them up when at full AP/HP/Stamina, but that's not the case so after all it feels random.
Normally the supplies are picked up automatically, but sometimes you just walk over them with no result.
Comments
The reason why it does not work sometimes is explained in this post:
http://nw-forum.perfectworld.com/showthread.php?677741-hunter-s-teamwork-bug-sort-of