I simply assumed the security recording we see at the beginning of the movie was faked. We're led to believe that The Operative is watching security footage the whole time we see the flashback. Disinformation is not beneath the Alliance and it gives them better credibility in making Simon a fugitive.
But he's a Parliament-level Operative. He has clearance higher than anyone in the Institute, hell, higher than anyone in the government. He's the one who'd be doing the deceiving, creating the fakes. And he'd be able to penetrate any attempt at a fake because he has the clearance to dig down to the deepest levels of the Institute's security systems.
Besides, Simon was already
a fugitive. He'd been under pursuit from the Blue Hands for eight months at the point the Operative was called in. Not to mention that he wasn't their real target; River was. Given the very real threat River posed, there was no point in playing up Simon as a fake threat so that people would go after him. They weren't supposed to go after him, they were supposed to go after River.
Also, you're getting it a bit backward. The whole time we're seeing the breakout, we're led to believe we're seeing it "live" or in flashback (depending on the viewer's prior familiarity with the series), but only when it pulls back to the Operative do we learn that it's actually security footage.
Here is a script excerpt from 'Serenity' (the pilot, not the film) that concerns Simon's explanation of why River was in that box:
Money. And luck -- for two years I couldn't get near her, but I was contacted by some men, some underground movement. They said she was in danger, that the government was playing with her brain. If I funded them they could sneak her out in cryo. Get her to Boros and from there, I could take her... wherever.
In the movie, as previously stated, Simon is directly
involved in River's escape, which, as shown by the above excerpt, is in direct contradiction of what was established in the 2-hour pilot. It is also slightly contradictory to his character development throughout the early episodes of the series, although not to any real detrimental degree.
Haven't we already covered this? Nobody's denying that a surface inconsistency exists, so there's no need to convince us. The point is that the change was done for a good and logical narrative reason, and that it's a minor enough discrepancy that it can be easily rationalized away. Any long-running fictional series contains contradictions; it's trivial to point that out. But it's okay as long as the contradictions are minor enough to be rationalized, or justifiable enough to be forgiven. And this is easily both.
Hirogen Alpha wrote:
Yeah, but it undercuts his character. He was a very smart guy--a genius, even--but in certain situations (romance, action) he is completely awkward and incompetent. While it is a cool moment in the movie to see Simon confidently impersonate an Alliance doctor, precisely drop the stun grenade, and confidently break River out, it doesn't line up with the television series. Not the television series I ever saw, anyway.
Did you not see "Ariel," then? Simon could be awkward and uncertain when he was out of his element, dealing with frontier situations and frontier people and getting caught up in other people's messy agendas. But when he was the one making the plans and setting the agendas, when he was in a situation where he understood the environment and was in control, he was ultracompetent. "Ariel" proved that beyond all doubt. He masterminded the whole operation to break into the hospital. He planned it down to the last detail and trained the rest of the crew in how to enact it. He was cool, collected, and completely in control throughout the operation. In short, he was the same Simon we saw in the Serenity
prologue. The only one who was awkward and incompetent there was Jayne, because now he
was the one who was out of his element.
And the other key thing about Simon's plan in "Ariel": he was doing it for River. No matter how clumsy or unsure he might be at other times, when it came to helping his sister, he was a force to be reckoned with. That was true in the series, and it was true in the movie. There's no contradiction, just a shift in emphasis.