Not sure how (von Mises) safety factor can be negative. Could you show an example? But yes, very low safety factors can be caused by badly shaped elements which tend to have greater error in stress for their size, sometimes quite extreme peaks. There might also be harmless stress singularities which you'd have to ignore the safety factor on.
Could you upload the .liml file? The only way I know of that von Mises stress or safety factor can appear negative is the interpolated values between nodes on quadratic elements. In that case, refine the mesh to reduce the error or ignore it if it's not significant. But that's a different problem from what Famous_Mortimer had since his errors were in the node or elements values.
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