diff --git a/subprojects/language/src/main/java/tools/refinery/language/validation/ReferenceCounter.java b/subprojects/language/src/main/java/tools/refinery/language/validation/ReferenceCounter.java
index 15fdf450..91624cd8 100644
--- a/subprojects/language/src/main/java/tools/refinery/language/validation/ReferenceCounter.java
+++ b/subprojects/language/src/main/java/tools/refinery/language/validation/ReferenceCounter.java
@@ -8,6 +8,7 @@
 import com.google.inject.Inject;
 import com.google.inject.Singleton;
 import org.eclipse.emf.ecore.EObject;
+import org.eclipse.emf.ecore.util.EContentsEList;
 import org.eclipse.xtext.util.IResourceScopeCache;
 import org.eclipse.xtext.util.Tuples;
 import tools.refinery.language.model.problem.Problem;
@@ -51,8 +52,14 @@ public static Map<EObject, Integer> computeReferenceCounts(EObject root) {
 	}
 
 	private static void countCrossReferences(EObject eObject, Map<EObject, Integer> map) {
-		for (var referencedObject : eObject.eCrossReferences()) {
-			map.compute(referencedObject, (key, currentValue) -> currentValue == null ? 1 : currentValue + 1);
+		var featureIterator = (EContentsEList.FeatureIterator<EObject>) eObject.eCrossReferences().iterator();
+		while (featureIterator.hasNext()) {
+			var referencedObject = featureIterator.next();
+			// Avoid double-counting the derived reference {@code variableOrNode} of {@code VariableOrNodeExpression},
+			// as the original reference is just {@code element}.
+			if (!featureIterator.feature().isDerived()) {
+				map.compute(referencedObject, (key, currentValue) -> currentValue == null ? 1 : currentValue + 1);
+			}
 		}
 	}
 }
diff --git a/subprojects/language/src/test/java/tools/refinery/language/tests/validation/VariableValidationTest.java b/subprojects/language/src/test/java/tools/refinery/language/tests/validation/VariableValidationTest.java
new file mode 100644
index 00000000..ae5f9e4f
--- /dev/null
+++ b/subprojects/language/src/test/java/tools/refinery/language/tests/validation/VariableValidationTest.java
@@ -0,0 +1,100 @@
+/*
+ * SPDX-FileCopyrightText: 2024 The Refinery Authors <https://refinery.tools/>
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ */
+package tools.refinery.language.tests.validation;
+
+import com.google.inject.Inject;
+import org.eclipse.emf.common.util.Diagnostic;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.params.ParameterizedTest;
+import org.junit.jupiter.params.provider.Arguments;
+import org.junit.jupiter.params.provider.MethodSource;
+import org.junit.jupiter.params.provider.ValueSource;
+import tools.refinery.language.tests.InjectWithRefinery;
+import tools.refinery.language.tests.utils.ProblemParseHelper;
+import tools.refinery.language.validation.ProblemValidator;
+
+import java.util.stream.Stream;
+
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.hamcrest.Matchers.*;
+
+@InjectWithRefinery
+class VariableValidationTest {
+	@Inject
+	private ProblemParseHelper parseHelper;
+
+	@Test
+	void shouldBeSingletonVariableTest() {
+		var problem = parseHelper.parse("""
+				pred foo(a, b).
+
+				pred bar(a) <-> foo(a, shouldBeSingleton).
+				""");
+		var issues = problem.validate();
+		assertThat(issues, hasItem(allOf(
+				hasProperty("severity", is(Diagnostic.WARNING)),
+				hasProperty("issueCode", is(ProblemValidator.SINGLETON_VARIABLE_ISSUE)),
+				hasProperty("message", containsString("shouldBeSingleton"))
+		)));
+	}
+
+	@ParameterizedTest
+	@ValueSource(strings = {"_shouldBeSingleton", "_"})
+	void singletonVariableTest(String variableName) {
+		var problem = parseHelper.parse("""
+				pred foo(a, b).
+
+				pred bar(a) <-> foo(a, %s).
+				""".formatted(variableName));
+		var issues = problem.validate();
+		assertThat(issues, not(hasItem(
+				hasProperty("issueCode", is(ProblemValidator.SINGLETON_VARIABLE_ISSUE)))));
+	}
+
+	@ParameterizedTest
+	@MethodSource
+	void shouldBeAtomNodeTest(String declaration) {
+		var problem = parseHelper.parse("""
+				pred foo(a, b).
+
+				pred bar(a) <-> foo(a, shouldBeAtom).
+
+				%s
+				""".formatted(declaration));
+		var issues = problem.validate();
+		assertThat(issues, hasItem(allOf(
+				hasProperty("severity", is(Diagnostic.ERROR)),
+				hasProperty("issueCode", is(ProblemValidator.NODE_CONSTANT_ISSUE)),
+				hasProperty("message", containsString("shouldBeAtom"))
+		)));
+	}
+
+	public static Stream<Arguments> shouldBeAtomNodeTest() {
+		return Stream.of(
+				Arguments.of("node(shouldBeAtom)."),
+				Arguments.of("declare shouldBeAtom."),
+				Arguments.of("multi shouldBeAtom.")
+		);
+	}
+
+	@ParameterizedTest
+	@MethodSource("shouldBeAtomNodeTest")
+	void shouldBeAtomNodeRuleTest(String declaration) {
+		var problem = parseHelper.parse("""
+				pred foo(a, b).
+
+				rule bar(a) ==> foo(a, shouldBeAtom).
+
+				%s
+				""".formatted(declaration));
+		var issues = problem.validate();
+		assertThat(issues, hasItem(allOf(
+				hasProperty("severity", is(Diagnostic.ERROR)),
+				hasProperty("issueCode", is(ProblemValidator.NODE_CONSTANT_ISSUE)),
+				hasProperty("message", containsString("shouldBeAtom"))
+		)));
+	}
+}