Can't speak to starting a mission without them, but if you're losing charges and you're playing in season 2, then it's probably the warp anomalies. For instance:

Veil of Carnage: An unique Warp creation, this anomaly will follow you after interacting with it.

• It will grant +400% damage bonus and +50% Supreme Movement Speed for 10 seconds.
• However, it will take away 2 of your Inoculator Charges and your slain enemies will have a 5% chance to come back from the dead as Demons!

These effects aren't listed anywhere in-game, but it is in the compendium.