There's few different reasons why it's seemingly impossible, but you usually end at around 99.95% - 99.98%:

• While all missions give you some upgrade items, one mission does not; thus you're missing six collectible boxes.
• There's a chaos object you need to destroy which simply doesn't exist (220 water towers in the game, 221 needed for 100%)
• you need to destroy some things multiple times, seemingly (random fuel shaft respawns after having been taken down once, some propaganda trailer might respawn); these are both doable if you know about these.

OK!