The defensive weakness
For both of the Man City goals, the King Power team were giving a winger too much time and space to make a choice. This occurred in the first due to James Justin being pulled astray by a running midfielder, and in the second by Hamza Choudhury making the same decision to pull inside. It is worth noting neither had the support of a primary winger or an aggressive centre-back to rush into that vacant space.
Nistelrooy has been perfectly fine with the Foxes conceding the wings. The thinking is that with the height of his central defenders and some midfielders there are few aerial situations they cannot at least make difficult or even go to win, and crosses into the box always have a chance for a good goalkeeper to make a challenge too. However, the second goal was a header from a well-placed cross, where Jannik Vestergaard and Hamza Choudhury were out of position.
Jakub Stolarczyk is also no Mads Hermansen. The Polish 'keeper has been excellent in my opinion. Solid when needed, but of course showing the need to improve his reactions and positioning, although the latter will come with experience more than anything. We cannot rely on having the Dane and also on the positioning of our defenders being correct every time. Pressure is critical. We did not apply any.
The solution to this would be a more progressive and aggressive centre-back on the right side dedicated to rushing forward into space and pressuring players. This would leave a gap in defence requiring one of the shielding midfielders to fall back. This could expose Leicester in other ways, but a new signing could be crucial in making this happen. Meanwhile, a mild systematic tweak depending on which wing the opposition is strongest down would also suffice.