You could get this warning when you have more estimates in the input file than expecated by proc mianalyze. This is likely to happen if you want to get the the differences between estimates from a model with interaction term. In a standard output from analysis proc (e.g. proc glm or mixed) you could then get a lot of comparisons but most likely you wouldn't be interested in all of them. For example you could get the LS Means Difference for say levels 1 vs 2 and 2 vs 1 but you would need only one. Please try and filter the input dataset (the one from analysis procedure) for the unique comparisons only - as defined by variables in your 'class' and 'modeleffects' statements - before reading into proc mianalyze and that should allow to get the summary out of proc mianalyze and you should get rid of the warning. If you were interested in summarizing all comparisons you would most likely need to sort the input dataset and use 'by' statment within proc mianalyze.
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