I think the problem in the second half was Modric and Rakitic were being given to much space. In the first half they both played much deeper than you’d expect. They were playing as the two centre midfielders in the system but spent more time closer to their defence than to the forwards. That was because of England’s pressing.
In the second half England started to sit deep and that afforded Modric and Rakitic more space to work in and so they started to play higher up with Rakitic especially playing closer to Perisic and Mandzukic. What Southgate needed to do in my opinion was bring off Alli and put on Loftus-Cheek and flip the midfield triangle. He should have put Loftus-Cheek alongside Henderson to sit in front of the three centre backs and have them move and backwards depending on the balls position and try to limit the space for Rakitic and Modric to play in. Then Lingard onto the right and Sterling back on the left to double up with the wing backs defensively. That would have meant a 541 out of possession but then Lingard and Sterling can carry the ball away from danger and lead counter-attacks.
Instead Southgate kept both Alli and Lingard as the centre midfielders and put Dier on for Henderson and the midfield problem just got worse.
In the second half England started to sit deep and that afforded Modric and Rakitic more space to work in and so they started to play higher up with Rakitic especially playing closer to Perisic and Mandzukic. What Southgate needed to do in my opinion was bring off Alli and put on Loftus-Cheek and flip the midfield triangle. He should have put Loftus-Cheek alongside Henderson to sit in front of the three centre backs and have them move and backwards depending on the balls position and try to limit the space for Rakitic and Modric to play in. Then Lingard onto the right and Sterling back on the left to double up with the wing backs defensively. That would have meant a 541 out of possession but then Lingard and Sterling can carry the ball away from danger and lead counter-attacks.
Instead Southgate kept both Alli and Lingard as the centre midfielders and put Dier on for Henderson and the midfield problem just got worse.