I was surprised when they benched Lee as well, but looking at his stats since the Highlanders game, I do think it makes more sense. He was putting in much more mixed performances after his strong debut.

Lee’s output across his first 4 games: a very busy start followed by a dip in productivity and accuracy
Lee’s standout qualities coming up through the grades (SRU20 & NZ U20) were his work rate at the attacking breakdown and his defensive volume. His first game against the Highlanders strongly mirrored those qualities (0.19 tackles per minute), with an added benefit of an increased carrying game (10 carries in 66 minutes).
Since then, however, both his volume and his accuracy have suffered, missing 4 tackles out of 17 against Moana and being limited to just 3 carries in 49 minutes against the Drua. I’m guessing the coaches felt he was hitting a wall somewhat.
Furthermore, Lee’s limitations from age grade rugby – his lack of dynamism on attack – have since resurfaced, beating just two defenders out of 30 carries and not making a whole lot of metres out of those carries (avg. 1.5m per carry per 80). I presume it’s one of the reasons Gardiner was preferred against the Reds, with the latter more dominant in contact on attack (8 defenders beaten out of 53 carries, or 15% carrying dominance versus Lee’s 6%).
Lee’s performance from the bench against the Reds was positive though, returning to his standards in both volume (0.19 tackles per minute) and accuracy (86% tackle success). It's obvious that the Crusaders flanker is a promising player but the consistency at SRP level is, understandably, not quite there yet.