Actually, I don't know what the problem is but I can say a bit about this situation.
As known, the results of the EM simulation can differ from the schematic results enormously. As I learnt from my professor, the most accurate and consolidated way to obtain compatible results with schematic and EM simulations is to proceed step by step. In other words, you shouldn't run an EM simulation after the overall circuit is built. Just take a part of the circuit by starting from the beginning, check schematic results and then, check EM results too. See the compatibility between them. Afterwards, go for adding the next few elements and do the same steps. Whenever the results go unexpected or bad, it can be thought that "there could be a problem in this related part".