(As I was typing this up, @Greatnoob on Twitter says that this simply isn't implemented yet. If that's the case, sorry if I wasted any time.)
On sites that have set their scale mode to "noscale" either in the swf, or in the HTML will incorrectly scale as the user pinches and zooms. This is exactly how Flash Lite used to work (and how it works on Wii last I checked). But on Android, they keep the size relative to containing HTML page, as this breaks many fewer sites. Based on observation, the on Android, Flash appears to be drawing to a bitmap, and allowing Android's WebKit to resize that bitmap. You can tell because it's all pixelated, like a cheaply scaled bitmap.
I hope this helps. :-)
Here are some example sites that have "noscale" set:
BTW, I'm using a build I found of 0.2 on some random blog. I'm not set up to compile iPhone apps yet, but I'd be happy to continue to test once I am.