Don't forget that as you use more equipment on a Mission, you increase the odds of some of it breaking.
So when you start and use just a few items per mission, your base odds are low. But I have one Mission where I now use 228 pieces of equipment (total, including consumables) every time. That jacks up the possibility of something going wrong and losing eqpt on that mission.
If you go back and try Missions with less equipment involved, I bet you'll see fewer losses. At higher levels though, Missions - especially your "go to" missions - really start stacking up the equipment and you see more frequent losses.