Random Losses

I've been experiencing this problem for quite some time and I cannot understand why at all. My ships are just randomly lossing supplies and ordanance and seem incapable of regaining it. Now I'm not stupid, supplies to deplete but does ordanance randomly go down when the ships are just moving from one planet to the next?? And the supplies that I do lose, they lose on a turn-basis rather than moving and losing it for each sector moved.
For example, my newly-created and glorious fleet is heading from my core system three systems out, and somewhere along the way (with no combat in between) they've lost all of their ordanance supply. Plus, the system they are in has two resupply depots that don't do a thing. Am I overlooking something? Please help.