Some apps have to run at startup or the phone won't work, so even if you stop them from startup, Android will load them. Otherwise, there's more than one startup app controller app.
(The only other way is to learn Linux and Android well enough to go into the files and modify them yourselves, to control what gets loaded automatically.)
I'm assuming that you don't have some if these "problem apps" set to start at boot in the apps themselves. That will cause them to start.