The left winger is going against the right defenseman. As Leafs fans are well aware, good RD are a scarce commodity in the NHL, and quite often you might have a left shot there which makes it much harder to keep the puck in.
This also doesn't account for the fact that Marner's line is likely to just be a high-event line in general, as well as his side of the ice. We need to separate the player's defensive play from the role/playstyle. Marner could have great shots against stats if they just trapped all game, but that wouldn't make him a better defensive player.
Conversely, you can ask how does Marner do relative to how other players would perform in a similar role? I'd bet that Phil Kessel's shots against chart looked much worse than that when he played here. Marner isn't a Selke-level defender, but he's definitely better than most offensive stars who play RW.