2. In the TV show, the doctor says that he paid some guys to get River out of the treatment facility via cryo. In the movie, he rescues her himself (which I found completely unbelieveable).
True, what Simon says
in the show contradicts what we saw in the movie, but people don't always tell the whole truth. Maybe Simon didn't want to admit that he'd broken her out himself. Maybe he thought that Mal would be less likely to keep Simon onboard if he knew that Simon was capable and devious enough to stage a successful commando raid on an Alliance intelligence facility. So he downplayed his role in River's liberation to make himself seem less threatening. (Though if he'd known Mal better, he might've done the opposite, since Mal would've admired anyone who could pull off such a feat against the Alliance.)
I don't buy this justification. Simon's characterization throughout the series was never one of an action hero like he's portrayed in Serenity. I don't see why he would lie about this detail, either. It just strikes me as inconsistent.
Which isn't as bad as the safe-word plot device, which would have come in infinitely handy during the series at a half-dozen instances, but of course never comes up because Whedon didn't conceive of this convenience until he needed it to advance the plot in Serenity.
Mal's behavior has already been mentioned. Doesn't strike me as consistent with the series (even if you throw in Those Left Behind--I haven't read Better Days and it looks like I'll be steering clear of it).
And its a minor detail, but the fact that Jewel Staite lost so much weight before the movie deflates some of the charm the character of Kaylee had in the series for me.