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You haven't provided much information, but I'm guessing your original design was in the ADS schematic editor. The layout view and simulator is a full-wave simulator, which takes into account things like parasitics and various transmission-line effects that your schematic might not have. The layout result, if you meshed properly, is more accurate.
If you used discretes (Caps, Inductors), this might be due to the size of the
Components. There's always potential for a little difference from simulation
Small Signal/ S-Param and layout 2.5D Simulation. The 2.5D sim is better
at higher frequencies (typically). You will have to do experiments to see
which methods are more accurate for yourself. i.e. put both circuits on
PCB and see which is better (if Possible)
This is not a issue, as @PlanarMetamaterials said the results of full wave simulator will not always be equal to Schematic simulator, you can use EMmodel instead of Schematic components to optimize to get exact values of EM results. Also your EM results(Layout) are accurate and close to real world designs.
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