I had the same issue, where WifiConfig GUI would not remember the deletion/removal of ssids in the Manage Networks tab. Raspbian doesn't have 'NetworkManager' settings but instead holds all network information (ssids, passwords, etc.) in
sudo nano /etc/wpa_supplicant/wpa_supplicant.conf
it's contents will look something like:
Once the file has been edited and saved reboot your pi for changes to take effect. Your pi will no longer attempt connection to the forgotten networks.
IF this file is empty, but your raspberrypi is still connecting to rogue networks, your credentials are likely held in the interfaces file:
sudo nano /etc/network/interfaces
The entries for ssids and networks looks a little bit different in here, but same idea. You should see them at the end of the file. They will look something like:
wpa-ssid "network name"
wpa-psk "wifi password"
Delete/Add as you see fit.