I think if I was looking at this objectively I'd say a couple things
1. England werent direct enough, with very few hard lines holding the defense from drifting, the kicking in behind was vastly overplayed, especially with overlaps, but England needed someone to just hit a line and make a 4 v 2 a 3 on 1, and they didnt do this well all day
2. Ben Youngs slow service really prevented using quick ball effectively, England quite often beat their forward counterparts round the corner, creating extra numbers and mismatches, and yet the defense was given extra time to set, meaning the attempted isolation of defenders looking at multiple options never really materialised, and he was a huge down point in this game. There was a 13 second ruck at one point. 13 bloody seconds
3. Until LCD mistake, England were at 6 penalties, and had conceded none in the first 20 mins of the second half, big improvement from them in this area
4. Rucking clearouts needed to be much much quicker at times, the ruck did on occasion get quite messy, even when England had made yards past the gain line
5. Marcus Smith has engineered a remarkable number of last minute comebacks this year, an outhalf isnt usually in a position of being exhausted at 60 mins, this was poor from EJ
6. Englands defense conceded off a smart Scotland lineout (Could be easily fixed) , with poor decision making on who to tackle from Isiekwe, and a penalty try that LCD maybe should have caught, held onto and conceded a penalty. In essence, England's defense was actually quite good this game