When the spark plugs are out of order what happens is that the fuel/air mix in the cylinder does not burn, instead it gets blown out of the exhaust valve, into your exhaust manifold, through your turbo (presuming you have one) and into your catalytic converter. This could potentially:
- foul the spark plugs
- gum up the exhaust valves
- foul the turbo (if present)
- ruin your catalytic converter
- damage the oxygen, gas temperature, and other sensors in the exhaust system
Any or all of these could happen over time, but it's unlikely they've happened to you in just 2-3km driven. Put the plugs in the right places and you should be good to go. AsIn your post you said that there was a drivetrain warning, which could be an indication something is wrong, so as it's just been serviced and any work done is under warranty, so I would take it back to them and get them to run a diagnostic on it to make sure it's all okay.