* The idea of the transwarp wave moving into the future as it spreads. Not only does it conveniently reach Predacon / Maximal Era Cybertron (or would have if the Tripredacus Council hadn't taken steps), but no explanation is given for why anyone picking it up wouldn't just travel back to immediately after the explosion, rather than weeks / months ''after'' it.
** It was stated at the beginning of the series that transwarp technology was experimental. They might still have been perfecting it.
* In ''Call of the Wild'', the beast mode glitch is repeatedly referred to as an issue specifically pertaining to Maximal programming... so why is Dinobot affected?
** In the first episode, he mentioned he'd reprogrammed his activation code to that of a Maximal, so maybe there's that.
** The Predacons are shown as, at best, second-class citizens, meaning that they have to make due with poorer technology and locales. It's possible that the Preds removed that particular glitch so they could adapt to life on more worlds. It might also explain why the first few battles tended to leave the Maximals running in fear: being more in tune with the mindsets of their (mostly) predator animal forms, they would have an advantage.
** Come to think of it, the glitch makes no sense at all. The Maximals primarily use their alt-modes to unobtrusively explore inhabited worlds. How would they do their studies on the local populations if they started tweaking out after a few days in beast-mode?
*** My guess would be that most inhabited worlds aren't as rich with raw Energon as proto-Earth, allowing the Maximals exploring them to be able to surreptitiously spend a good amount of time in robot mode to compare notes with their comrades. Either that, or the glitch is a side-effect of the presence of excess ambient Energon radiation.
*** You also have to take into account that the glitch only comes up because they have to stay in their alt-modes for days to protect themselves from Energon poisoning. As explorers, they would have hidden their ship and be returning to it during downtime each day where they could safely return to robot mode and the ship's shields would protect them from any dangerous radiations.
* Near the end of the run, Megatron transforms into a dragon. This seems completely bizarre as dragons didn't exist in Earth history... until you rewatch G1 episodes like "A Decepticon In King Arthur's Court" and realize that dragons actually did exist in Earth's history. Megatron might very well have scanned a lifeform best suited for his needs while in the lava (okay, it doesn't explain everything, maybe he internalized a previous scan but was not able to make the shift yet due to time concerns, but it's not COMPLETELY out of left field).
* One would think by destroying Optimus Prime, you'd run the risk of losing the Matrix of Leadership and letting Unicron destroy Cybertron. But you must realize, the plan was made by ''Megatron''. Megatron ''becomes'' Galvatron, meaning he made this plan ''before'' they found out about Unicron. This plan would have given the Decepticons victory... until Unicron decides to come along and chow down on Cybertron.
** Given that the Predacons were unaffected by the time storm, this implies that not only do the Decepticons defeat the Autobots, but they also beat Unicron as well, without the use of the Matrix!
*** It could have been a delayed reaction of sorts. The Maximals were disappearing first since Optimus Prime, the Maximals' ancestor was dying, but if the altering of the timeline continued unopposed the Predacons would likely have gone next.
* Waspinator's apparent invincibility was mostly a running gag, but considering he was possessed by the immortal Starscream it is possible he came away from the experience with similar capabilities.
* Despite having a spark said to be indestructible, Depth Charge is able to destroy Rampage's spark by ramming a spike of energon into it. At first this seems like an error, considering Megatron was able to use an energon blade to divide Rampage's spark in two to no ill effect. But when Rampage dies Dinobot is able to sense it and notes that he finally feels whole. Rampage's spark ''wasn't'' destroyed, half of it was and the other half regenerated to compensate.
* In "Optimal Situation", when Optimus first received his "Optimal" body, he kicked ass and took names of all the Predacons, [[TheWorfEffect but for the rest of the season, Optimus lost many of his fights]]. Perhaps Optimus Prime's spark lent him lots of power. This is especially noteworthy when he fights the Transmetal 2 Megatron, who had the spark of G1 Megatron in him, in the last few episodes.
* This one mostly affects the toys, but there's a small crab figure named Razorclaw. Now, in G1, the original Predacons included a lion named Razorclaw and a tiger named Rampage. So Beast Wars ''also'' has a Razorclaw and a Rampage who turn into similar animals, the main difference being one is a lot bigger. However, which is which is different.
* In ''Transformers WesternAnimation/BeastWars'', you have Megatron cutting Rampage's spark in half, then keeping half of said spark in a box lined with energon spikes, squeezing it to cause him immense pain whenever he gets out of line. The horror comes when you remember that, for all intents and purposes, sparks=souls. Megatron essentially tore half of Rampage's soul out of him. And that's not even getting into creating Dinobot II with said half of soul.
** Speaking of Rampage, let's not forget how he became a monster, in the first place; ''the Maximals experimented on him in an attempt to copy the immortality of [[TheStarscream THE Starscream]], the worst Decepticon opportunist in existence.'' Yes, the ''good guys'' performed Nazi-esque eugenics experiments on ''their own people'' in an attempt to emulate the conditions of ''one of the most notorious bad guys of their era''. Then remember that they ''also'' pulled a BigBrotherIsWatching by locking down all information and locations related to the Great War, keeping ''their own people'' ignorant of their past. All in the name of not reliving the atrocities of that war. HeWhoFightsMonsters, indeed...
*** Can't it be considered ProperlyParanoid when the first thing a capable Predacon leader does when getting hold of the location of Earth was to head there with the explicit intent to go back in time and kill the Autobots in stasis lock? Meanwhile, Starscream wasn't always a megalomaniac, he used to be a scientist. Could you condemn someone just because they share a similar origin to someone horrible (or did they explain somewhere that whatever turned Starscream immortal also turned him treacherous and megalomaniacal?)
*** No, because the Predacon records were never sealed, so any Predacon who cared easily learned what happened on Earth (Megatron Dinobot, even Blackarachnia who was 'born' on Earth). It's just that messing with time on that scale is considered insane and over the line even to the Predacons, Megatron was just that crazy and his minions too uninformed about his real motives. You'll notice the only other Predacons who understood what he was doing were Tarantulas, who wanted EVERYONE to die, and Dinobot, who died trying to stop Megatron from manipulating time.
* A somewhat minor example, but when Rhinox is deprogrammed in ''Dark Designs'', he comments about how being a Predacon is "like being three gigs of attitude on a two gig hard drive. No wonder they've got personality problems", leading to an EverybodyLaughsEnding... save for Dinobot, who is a Maximal by choice, not by programming, and who is still immensely proud of his Predacon heritage (Megatron and his merry band of lunatics, not so much). What Rhinox said would be immensely insulting to someone like that.
** Of course, earlier in the episode, Cheetor's reaction to Rhinox's programming was "Better dead than Pred", which led Dinobot to retort "Some of us have survived the experience", so that isn't entirely overlooked.
* The existence of new Predacons as the series goes on is pretty horrible, when you think about it. At the start of the series, before they crash land on Earth the Maximals jettison their hibernating crew members in their stasis pods to protect them from the crash and energon on the planet, planning to pick them up after they sort out the whole mess. New characters are introduced in the series by having some of these pods crash to Earth, and the Maximals and Predacons fight over them. So far, every single awakened character has no memory of their time on Cybertron due to damage from the crash. But the Predacons take it one step further and purposely [[BrainwashedAndCrazy wipe their memories and implant a program]] that makes them aggressive, scheming, and all the other things that Megatron wants in a minion. As shown in the last few episodes, if the program is removed, it kills the Predacon in was implanted in. That means that Inferno, Blackarachnia, and Quickstrike were probably all loyal Maximals at one point, and all much different people than what they were forced to become.