You should turn off the option in iTunes to automatically download purchased apps if you are using the same iTunes account. iCloud accounts are different from iTunes accounts.
wifi sync with iTunes is the same as if you plugged in your phone to the physical computer. If the app has been auto downloaded because you told iTunes to do this after it was purchased on the phone, then the next time another iPhone is plugged in to iTunes or wirelessly synched, its going to install the app. This is something to turn off in iTunes and not the individual phone.