With the stereo, the wires are all independent of the ECU except the CANBUS wires. There are two wires in the main plug for CANBUS purposes.
With the factory headunit, the CANBUS wires have various functions:
*sending radio data to the multifunction display (ie: track number, etc)
*turning on/off with ignition
When installing an aftermarket headunit, the CANBUS wires are not used. They serve no function with an aftermarket headunit.
The only reason I could imagine where your new headunit is causing probs, is if the installer decided for some unknown reason to connect the new headunit to the CANBUS wires (and therefore 'feeding back' inappropriately to the ECU; even then, for it to trigger the MSCF error seems remote). An experienced installer would never do this, because there is no logic to it, and they would have to be 'guessing' to do it (ie: not know what they are doing).
There are 5 plugs for the factory headunit, though the 2 main ones are joined as a single 'double plug' and the 3 mini plugs slot together as a single 'triple plug':
1. powerwire ISO plug: which includes the two CANBUS wires in positions A1 and A3
2. speakerwire ISO plug: 8 speakerwires
3. yellow mini-ISO plug: goes to Bose amp if you have Bose
4. green mini-ISO
5. blue mini-ISO: for CD changer
The green mini-ISO plug has 6 wires, 3 of which are for the steering wheel controls
C10 = RC-A
C11 = RC-B
C12 = groundwire
A steering wheel control interface (stalk control interface) will plug into the green mini-ISO plug and 'translate' the Alfa signals to be compatible with your new headunit. The SWCI then connects to your new headunit via a patch lead that has the right plug on the end to fit the socket on the back of the headunit.
Hope that helps.