I understand that. But why? Some Apps transfer fine and some don't.
I'm not sure I follow you...
1) For any app that is
iPhone compatible,
which you installed via Apple's app store, you transfer it by plugging the iPad into a computer, syncing the app onto the computer, and then plugging in the iPhone and syncing it.
2) Any app that is
not iPhone compatible, even if it came from the App Store, will not install on the iPhone, for reasons that are hopefully obvious.
3) Any app that you installed on your iPad, which is iPhone compatible but did not come from the app store, was installed using some Jailbreak install mechanism, and
these apps will not be installable on your iPhone unless you jailbreak it. Once you jailbreak your iPhone, then there should be some tools you can install that will let you sync jailbreak apps from the iPad to a computer and then to the iPhone.
4) Hopefully the final case, of apps that are both not from the app store and are also not iPhone compatible, does not need further discussion.