The applications should ask whether or not to connect to the internet (and how - e.g. prefer WLAN, ask for UMTS). It has been observed that an UMTS connection was established, without asking for permission or giving a notification. As this can lead to potentially high costs for the user, great care has to be taken.
We need more infos on how this happens and the exact connection settings on the phone. It's not reproduceable on multiple N900's here, nor do we have code that explicitly modifies the online state of the phone, let alone overwrite user preferences.