This isn't a huge deal, just a minor annoyance
For instance, I set the max atlas size to 1024 and it says it can't pack everything into the atlas. I set the max atlas size to 2048 and it works fine... and spits out an atlas that's 1024x1024. So obviously it CAN fit everything, but maybe the check for this is/isn't taking something into account when it should/shouldn't?
I've noticed sometimes the padding on sprites can keep it from fitting them into the atlas, even when the atlas's texture mode is set to clamp (so there's no padding needed on the edge). Maybe this has something to do with it?