BUG: Fix return of missing values when applying loc to single level of MultiIndex

doc/source/whatsnew/v1.2.0.rst

@@ -466,6 +466,7 @@ Indexing
 - Bug in indexing on a :class:`Series` or :class:`DataFrame` with a :class:`MultiIndex` with a level named "0" (:issue:`37194`)
 - Bug in :meth:`Series.__getitem__` when using an unsigned integer array as an indexer giving incorrect results or segfaulting instead of raising ``KeyError`` (:issue:`37218`)
 - Bug in :meth:`Index.where` incorrectly casting numeric values to strings (:issue:`37591`)
+- Bug in :meth:`DataFrame.loc` returned requested key plus missing values when ``loc`` was applied to single level from :class:`MultiIndex` (:issue:`27104`)
 
 Missing
 ^^^^^^^

pandas/core/indexes/base.py

@@ -3842,9 +3842,9 @@ def _get_leaf_sorter(labels):
         else:
             left_lev_indexer = ensure_int64(left_lev_indexer)
             rev_indexer = lib.get_reverse_indexer(left_lev_indexer, len(old_level))
-
+            old_codes = left.codes[level]
             new_lev_codes = algos.take_nd(
-                rev_indexer, left.codes[level], allow_fill=False
+                rev_indexer, old_codes[old_codes != -1], allow_fill=False
             )
 
             new_codes = list(left.codes)

pandas/tests/indexing/multiindex/test_loc.py

@@ -598,3 +598,15 @@ def test_getitem_loc_commutability(multiindex_year_month_day_dataframe_random_da
     result = ser[2000, 5]
     expected = df.loc[2000, 5]["A"]
     tm.assert_series_equal(result, expected)
+
+
+def test_loc_with_nan():
+    # GH: 27104
+    df = DataFrame(
+        {"col": [1, 2, 5], "ind1": ["a", "d", np.nan], "ind2": [1, 4, 5]}
+    ).set_index(["ind1", "ind2"])
+    result = df.loc[["a"]]
+    expected = DataFrame(
+        {"col": [1]}, index=MultiIndex.from_tuples([("a", 1)], names=["ind1", "ind2"])
+    )
+    tm.assert_frame_equal(result, expected)