Alternative Character Interpretation: Did Doofenshmirtz-2 really turn evil because he lost that toy train? Or did he have a past so unbelievably traumatic that he blocked it out, and funnels all those negative emotions into the loss of his beloved childhood toy? Or was he a horrible person even as a kid and is just using the train as an excuse?
Broken Base: Phineas' characterization in the movie proved to be divisive. Phineas is almost never upset or angry (GET ON THE TRIKE!! notwithstanding); here, he's mad at Perry for half the movie's run time. It's presented as OOC Is Serious Business (he believes his entire bond with his beloved pet was a lie), but to some fans, it came across as cruel, unwarranted, and thoroughly un-Phineas-like.
Ensemble Dark Horse: Of all the 2nd dimension characters, Candace-2 is the most loved. No surprise if you consider that she is a badass Action Girl and just about everything she does is a moment of awesome.
They Wasted a Perfectly Good Plot: What? No Vanessa (Original and Parallel) and/or Parallel Stacy? No Parallel Stacy is even more of one when you realize that her absence is justified since Parallel Candace's "growing up" so fast probably made it so that she never met her world's Stacy, which makes the plot an even bigger waste because Original Candace and Stacy never bring that up or reflect on it.
In a way, they already used that plot with Parallel Jeremy (While she did meet him, she thought of him purely as a soldier, rather than a possible friend or boyfriend like she would have had she not had to grow up so fast.) Throwing in the same thing with Stacy would have wasted time without adding much.
And there was going to be a few scenes with both original and parallel Vanessa, but they had to cut them out due to timing. You can watch said deleted scenes on the DVD. Alleviated in the sequel episode, in which a major part of the episode continues off of parallel Vanessa's missing scene.
Ferb's role is pretty downplayed, and he doesn't really respond to the fact that Perry has (to their information) betrayed him just as much as Phineas. Similarly, he doesn't do much in the final battle, showing up after everything is already done.
What an Idiot!: Lampshaded in-universe. Our Doof once built an army of robots just like Doof-2, except he 1) installed self-destruct switches and 2) placed them on the bottom of their feet so no one would be able to reach them. One step later and...