It isn't just about the goal against Southampton, we've seen Lindelof lose several 'key' challenges because he's too much a gentleman, not physical enough. He is a very clean and correct player. 2 yellow cards in 50 games as a CB tells you a lot.
Since he was signed I've seen him bullied on many occasions by lesser players. He does have a good read of the game and that's why he does well against 'ball playing' teams but when it gets physical he usually gets overwhelmed. All the better PL Center-backs have a little mean-streak in them, they pinch and pull, shove and push. Lindelof on the other hand tries to play by the book ending up getting destroyed by players like Mooy, Deeney etc. Sadly for us and him the PL is high paced and very physical.
He's not lacking in skills imo, but in toughness which I believe is hard to get by training, it's a mental aspect he doesn't possess.