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.
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 unobtrusivley 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.
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 this 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 it 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, 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 Beast Wars, 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 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 Big Brother Is Watching 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. He Who Fights Monsters, indeed...
Can't it be considered Properly Paranoid 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?)
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 Everybody Laughs Ending... 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.