The Mechanical Fatigue Tool (FT) uses the raw nodal stresses to predict the fatigue life. If you have a local "hot spot" in the model (for whatever reason - bad mesh, stress singularity, etc.), the FT will use that local stress in the fatigue calculations. You probably should remove that hot spot from the FE model. If removing it is impractical, then you should probably remove that node(s) from the fatigue calculations by scoping the results to a Named Selection that does not contain that node(s).
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