diff --git a/tests/test_partitioning.py b/tests/test_partitioning.py
index c72b13f5b..19b3a3b4c 100644
--- a/tests/test_partitioning.py
+++ b/tests/test_partitioning.py
@@ -141,7 +141,7 @@ def test_merge_partitions__errors(self):
         partitions[1]["extra"] = (grid1.face_dimension, np.ones(grid1.n_face))
         with pytest.raises(
             ValueError,
-            match="'extra' does not occur not in all partitions with 'mesh2d'",
+            match="Missing variables: {'extra'} in partition",
         ):
             pt.merge_partitions(partitions)
 
diff --git a/xugrid/ugrid/partitioning.py b/xugrid/ugrid/partitioning.py
index 839fbed5e..2edc350f3 100644
--- a/xugrid/ugrid/partitioning.py
+++ b/xugrid/ugrid/partitioning.py
@@ -214,19 +214,6 @@ def validate_partition_objects(
     return None
 
 
-def validate_vars_in_all_data_objects(
-    vars: list[str], data_objects: list[xr.Dataset], gridname: str
-):
-    for var in vars:
-        var_in_objects = [
-            True if var in obj.variables else False for obj in data_objects
-        ]
-        if not all(var_in_objects):
-            raise ValueError(
-                f"'{var}' does not occur not in all partitions with '{gridname}'"
-            )
-    return None
-
 
 def separate_variables(objects_by_gridname: defaultdict[str, xr.Dataset], ugrid_dims: set[str]):
     """Separate into UGRID variables grouped by dimension, and other variables."""
@@ -276,22 +263,45 @@ def all_equal(iterator):
     return grouped, other
 
 
-def maybe_pad_connectivity_dims_to_max(selection, merged_grid):
-    nmax_dict = merged_grid.max_connectivity_sizes
-    nmax_dict = {
-        key: value for key, value in nmax_dict.items() if key in selection[0].dims
-    }
-    if not nmax_dict:
-        return selection
-
-    pad_width_ls = [
-        {dim: (0, nmax - obj.sizes[dim]) for dim, nmax in nmax_dict.items()}
-        for obj in selection
-    ]
-
-    return [
-        obj.pad(pad_width=pad_width) for obj, pad_width in zip(selection, pad_width_ls)
-    ]
+def merge_data_along_dim(
+    data_objects: list[xr.Dataset],
+    vars: list[str],
+    merge_dim: str,
+    indexes: list[np.array],
+    merged_grid: UgridType,
+) -> xr.Dataset:
+    """"
+    Select variables from the data objects.
+    Pad connectivity dims if needed.
+    Concatenate along dim.
+    """
+    max_sizes = merged_grid.max_connectivity_sizes
+    ugrid_connectivity_dims = set(max_sizes)
+
+    to_merge = []
+    for obj, index in zip(data_objects, indexes):
+        # Check for presence of vars
+        missing_vars = set(vars).difference(set(obj.variables.keys()))
+        if missing_vars:
+            raise ValueError(f"Missing variables: {missing_vars} in partition {obj}")
+
+        selection = obj[vars].isel({merge_dim: index}, missing_dims="ignore")
+        
+        # Pad the ugrid connectivity dims (e.g. n_max_face_node_connectivity) if
+        # needed.
+        present_dims = ugrid_connectivity_dims.intersection(selection.dims)
+        pad_width = {}
+        for dim in present_dims:
+            nmax = max_sizes[dim]
+            size = selection.sizes[dim]
+            if size != nmax:
+                pad_width[dim] = (0, nmax - size)
+        if pad_width:
+            selection = selection.pad(pad_width=pad_width)
+
+        to_merge.append(selection)
+
+    return xr.concat(to_merge, dim=merge_dim)
 
 
 def merge_partitions(partitions):
@@ -353,21 +363,11 @@ def merge_partitions(partitions):
             other_vars_obj = set(other_vars).intersection(set(obj.data_vars))
             merged.update(obj[other_vars_obj])
 
-        # Now remove duplicates, then concatenate along the UGRID dimension.
         for dim, dim_indexes in indexes.items():
             vars = vars_by_dim[dim]
             if len(vars) == 0:
                 continue
-            validate_vars_in_all_data_objects(vars, data_objects, gridname)
-            selection = [
-                obj[vars].isel({dim: index}, missing_dims="ignore")
-                for obj, index in zip(data_objects, dim_indexes)
-            ]
-            selection_padded = maybe_pad_connectivity_dims_to_max(
-                selection, merged_grid
-            )
-
-            merged_selection = xr.concat(selection_padded, dim=dim)
+            merged_selection = merge_data_along_dim(data_objects, vars, dim, dim_indexes, merged_grid)
             merged.update(merged_selection)
 
     return UgridDataset(merged, merged_grids)