- Two enemies that appear in the medieval levels are frogs (when they collide with Crash and kiss him, it's revealed that they were princes cursed by magic) and wizards (that fire magic at Crash, which turn him into a frog if he collides with it). It stands to reason that these wizards are the reason the princes have all been turned into the various frogs that inhabit the levels in the first place. On closer inspection, the princes and the wizards both resemble the scientists of the previous two games (that this game reveals are basically cloned in the secret warp room). Cortex's allies are basically turning on each other; it's no wonder he's never successful.
- The final boss, Cortex, has three hit points. Each time he goes down, Uka Uka revives him to get him back into the fight. This mirrors how Aku Aku is Crash's protection mask, with a full-powered Aku Aku mask being able to shield Crash two times before Crash is vulnerable again. The same is true for Cortex and Uka Uka. Uka Uka can only protect him twice, and Cortex goes down for good when Crash put him down the third time.
- The final phase's attack patterns where both Aku and Uka cause explosions aiming for Crash's current location may seem like the game making the boss more challenging, but seeing the N sane version made this troper realize. Uka is trying to take out Crash himself, only for Aku to (try to) intercept his attack to protect Crash!
- The 100% ending. Cortex and Tropy are turned into babies, sitting in the middle of a chunk of land with gas spewing up from the craters, and with the background of the warp hole; in other words, nowhere. Though they still manage to make it funny by having them fighting over Uka Uka in a tug-of-war.
- The levels Bye Bye Blimps and Mad Bombers are set in WW1 Europe. Yeah, one of the bloodiest and deadliest wars in the history of mankind. And the protagonist never cease to smile.
- Cortex was implied to have lost all allies but N. Gin in the events of the second game, relying on tricking Crash to do his dirty work. By the start of this game, he already has minions, Tiny and Dingodile tending to the mission. Dingodile is a random new introduction Cortex inexplicably created in the short point after Uka Uka's release, while Tiny was originally N. Brio's associate working against Cortex (ironically in this and all later games, Tiny is Cortex's most faithful henchman).
- The whole point of the Time Travel Framing Device is that Uka Uka wants to get the Crystals and Gems from their original locations in time. Ignoring the potential for Temporal Paradoxes this invites, several levels take place in the future. While you could Hand Wave that in these cases you're gathering the future versions of the Crystals, that explanation takes the Timey-Wimey Ball and starts playing kickball with it (for one thing, couldn't there then be 50 Crystals, 25 in the past and 25 in the future?)
- FridgeBrilliance: Maybe the crystals take a while to form underground, and they weren't fully formed in the current timeline? After all, the intro to 2 shows that they can certainly grow in caves.