The red exclamation mark is reapplied to Upgrades every time you buy a Resistance thing for which you did not buy the latest upgrade, even if nothing new appeared.
Ultimate Ninja upgrade has a slightly wrong description: it also boosts click gain.
Upgrades stop appearing too early for that 1 billion cost to be approachable.
Nice work on the graphics! Though, as others said, the mechanics and game numbers are not exactly new.