Pretty sure it's all about the neck of the bottle. Some bottles (such as Sam Adams, Sweetwater and most other traditional "long necks") have a long "bump" at the top of them, which is ideal for a wing capper.
Some bottles have a medium "bump" on them which seem to work okay for me. (Such as New Belgium's bottles)
I've stopped trying to use Lagunitas bottles. Sierra Nevada bottles aren't much better. If you have one handy, look at the neck on it. The part that the wing capper "grabs" is very short and doesn't let the bell push down very hard.
If you look at the bottles you're trying to cap, I'd be willing to bet that the bombers with the big dimple in them have a long "bump" at the top and the ones with without an indentation have a shorter "bump".
Here's a pic (not mine) to demonstrate:
The bottle on the right is the best kind of neck for a wing capper.