BUG: fix silent DataFrame.melt corruption on var_name collisions

doc/source/whatsnew/v3.1.0.rst

@@ -370,6 +370,7 @@ Groupby/resample/rolling
 Reshaping
 ^^^^^^^^^
 - Bug in :func:`merge` where merging on a :class:`MultiIndex` containing ``NaN`` values mapped ``NaN`` keys to the last level value instead of ``NaN`` (:issue:`64492`)
+- Bug in :meth:`DataFrame.melt` where ``var_name`` colliding with an ``id_vars`` column or ``value_name`` silently overwrote the affected column data instead of raising (:issue:`65654`)
 - Bug in :meth:`DataFrame.pivot_table` with ``margins=True`` raising ``TypeError`` when ``values`` has an :class:`ExtensionDtype` that cannot hold ``NA`` (e.g. :class:`IntervalDtype` with an integer subtype) and no ``columns`` were specified (:issue:`55484`)
 - Bug in :meth:`Index.union` where the result could be unsorted when both inputs were monotonic increasing but disjoint, when ``sort`` was not ``False`` (:issue:`54646`)
 - In :func:`pivot_table`, when ``values`` is empty, the aggregation will be computed on a Series of all NA values (:issue:`46475`)

pandas/core/reshape/melt.py

@@ -240,6 +240,21 @@ def melt(
     else:
         var_name = [var_name]
 
+    output_names = (*id_vars, *var_name, value_name)
+    if len(set(output_names)) != len(output_names):
+        seen = set()
+        dups = []
+        for n in output_names:
+            if n in seen:
+                dups.append(n)
+            else:
+                seen.add(n)
+        raise ValueError(
+            f"melt would produce duplicate column names {dups} from "
+            f"id_vars={id_vars!r}, var_name={var_name!r}, "
+            f"value_name={value_name!r}."
+        )
+
     num_rows, K = frame.shape
     num_cols_adjusted = K - len(id_vars)
 

pandas/tests/reshape/test_melt.py

@@ -563,6 +563,22 @@ def test_melt_duplicate_column_header_raises(self):
         with pytest.raises(ValueError, match=msg):
             df.melt(id_vars=["A"], value_vars=["B"])
 
+    @pytest.mark.parametrize(
+        "kwargs",
+        [
+            {"id_vars": "id", "var_name": "id"},
+            {"id_vars": "id", "var_name": "x", "value_name": "x"},
+            {"id_vars": ["id", "variable"], "value_vars": ["a"]},
+        ],
+    )
+    def test_melt_var_name_collision_raises(self, kwargs):
+        # GH 65654
+        df = DataFrame(
+            {"id": [1, 2], "variable": [9, 9], "a": [10, 20], "b": [100, 200]}
+        )
+        with pytest.raises(ValueError, match="duplicate column names"):
+            df.melt(**kwargs)
+
 
 class TestLreshape:
     def test_pairs(self):