diff --git a/@ensemble/loadSettings.m b/@ensemble/loadSettings.m
index e18f79ea..8adbd4dd 100644
--- a/@ensemble/loadSettings.m
+++ b/@ensemble/loadSettings.m
@@ -29,6 +29,9 @@
     notEnoughMembersError(max(members), nEns, obj.file);
 end
 
+% Return the variable indices in sorted order
+v = sort(v);
+
 end
 
 % Long error messages
diff --git a/@ensemble/useVariables.m b/@ensemble/useVariables.m
index 4a23fb16..efafcfb3 100644
--- a/@ensemble/useVariables.m
+++ b/@ensemble/useVariables.m
@@ -23,7 +23,7 @@
 else
     obj.stateVector.checkVariables(varNames);
     varNames = string(varNames);
-    varNames = unique(varNames(:), 'stable');
+    varNames = unique(varNames(:));
 end
 obj.variables = varNames;
 
diff --git a/@ensembleMetadata/extract.m b/@ensembleMetadata/extract.m
index c34668b6..790c9bd7 100644
--- a/@ensembleMetadata/extract.m
+++ b/@ensembleMetadata/extract.m
@@ -13,6 +13,7 @@
 % obj: The updated ensembleMetadata object.
 
 % Error check, variable indices
+assert(~isempty(varNames), 'varNames cannot be empty');
 v = dash.checkStrsInList(varNames, obj.variableNames, 'varNames', 'variable in the state vector');
 
 % Get the variables to remove