Using the transporter tool between BES 4.1 and 5.02 without any demanded changes (to policy or so on) results in a bunch of garbage being installed on our end users devices.

I tried making a policy that blocked App center, BB app world, and a few other things without luck.

If anyone knows how to avoid this please advise.

its not the transporter tool, you have misconfigured your it policy. the carriers push these icons down (which are actually just shortcuts to download the applications, nothing is really installed). they have likely been there the entire time, you just didnt realize it because the policy was set on the other bes.

set allow application download services to no in the browser section of the it policy.

That was exactly right. Thanks! I would not have thought it would be found under "browser"