At the end of Chapter 3, Optimus encounters Starscream while trying to disable the last Decepticon Warp Cannon. This may come as a surprise to most players, but an Easter Egg proves otherwise. A quick easter egg can be found after Metroplex saves Optimus from the three Leapers. In an area with several turrets, looking at the one with Laserbeak on it will reveal it to be Soundwave, who taunts you before leaving. Considering that this was right before the final turret area, no wonder why Starscream found you.
In Chapter 9, Soundwave uses Dark Energon to revive Megatron. While Dark Energon in Transformers Prime does re-animate the dead, it also causes adverse side-effects. So how come Megatron doesn't turn into a Terrorcon? In Transformers: War for Cybertron, Megatron fused his spark with Dark Energon and survived. Since his body had already accepted Dark Energon into its system, Megatron wasn't corrupted as easily.
Why is the Insecticon's chatter understandable when playing as Grimlock and not when playing as Jazz? Shockwave likely added the ability to him.
At the end of Chapter 12, you have the opportunity to explore Shockwave's lab and hear his analyses of Earth and Dinosaurs. The main feature of this room, which actually triggers a small cutscene is a hologram of Sludge's dino body. Now, we know that Sludge didn't survive the Insecticon attack, but there is a slight implication that Shockwave had planned the "experiments" before actually capturing the Lightning Strike Coalition Force. If he's now focusing his attention on Sludge, the dino that never happened, it's likely that he's just adapting the design for another guinea pig. He had more prisoners.