Here's something I found that was odd, but I don't know if it would necessarily qualify as a "bug" exactly...
Check out my burst.cap (located in this thread).
In v0.98.9 the swarm of sprites looks like this, all nice and evenly distributed:
<img src="http://i40.tinypic.com/2gtclcx.png">
But if you run it in v0.99 it looks all lopsided like this:
<img src="http://i41.tinypic.com/54t4s8.png">
It's like the sprites are favoring the right side of the swarm, as though they're choosing to turn in that direction more often. It's kinda weird, but like I said I don't know if this is what you would call a bug, or what might have been changed in 0.99 to make it do that.
Edit:
Whoa, I just noticed there's actually a big difference in the way the images are rendered too. The 98.9 version looks more, er... compact. If that makes any sense. The 0.99 version definitely looks like the alpha on the additive sprites is spreading out more. Strange.