Cybertronium Deficiency: Cybertonium is a green, crystalline element found only on Cybertron and is used in the construction of Transformer bodies on that planet. If Scavenger is deficient in Cybertronium, it will cause minor malfunctions, at first, such as an inability to fully transform or control one's actions, but if the depletion proceeds past a critical level, it can lead to death.
Damaged Spark: While Scavenger is capable of living for centuries, he can still be killed if his spark is damaged. However, it is possible to bring Scavenger back to life with the AllSpark or Energon.
Alien Technology: Any alien technology is perfectly capable of killing Scavenger even from weapons of his design.
Extreme heat/cold: Scavenger can adapt to any environment he comes across and survive anything for a longer time than a human. However, he is still capable of suffering from further damage if suffering from prolonged exposure. This includes shutting down into stasis until they are moved to a warmer location.
Heavy artillery: Some human weapons can kill Scavenger through heavy artillery, as seen with William Lennox and his comrades taking out Blackout with a bazooka gun and Sam managing to kill Starscream with a broomstick he stuck in his eye. A single wound from the AllSpark by merging with Construction’s spark will kill them but the Cybertronian can still be brought back to life.
Leaking Energon: Energon is the preferred fuel/energy source of Transformers. It has also been shown as food, intoxicating drink, ammunition, and even currency. Much like water is for humans, Scavenger and his race depend on Energon as a fuel source and an Energon leakage can be dangerous for them.
T-cog dependency: Scavenger depends on a T-cog, which grants them the ability to transform between a vehicle form and a bipedal form. However, if Scavenger is without his T-cog, he will be unable to transform, blend in with his surroundings on an alien planet, and be immediately exposed.
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