"AssertionError: Gaps in blk ref_locs" when unstacking filtered DataFrame

[toobaz]

Code Sample, a copy-pastable example if possible

In [2]: df = pd.DataFrame([[2009, 1, 15, 'City1', 'Housing'],
   ...:                    [2010, 2, np.nan, 'City2', 'Housing']],
   ...:                   columns=['year', 'month', 'day', 'city', 'sector'])
   ...:                   

In [3]: df['day'] = 15
   ...: df['date'] = pd.to_datetime(df[['year', 'month', 'day']])
   ...: 

In [4]: ind = df.set_index(['date', 'sector', 'city'], drop=False).sort_index()

In [5]: 

In [5]: cols = ['month', 'year', 'sector']
   ...: per_city = ind.loc[(slice(None), slice(None), 'City1'), cols].dropna(how='any')
   ...: 

In [6]: per_city.unstack()
---------------------------------------------------------------------------
AssertionError                            Traceback (most recent call last)
<ipython-input-6-97028d1092eb> in <module>()
----> 1 per_city.unstack()

/home/nobackup/repo/pandas/pandas/core/frame.py in unstack(self, level, fill_value)
   4575         """
   4576         from pandas.core.reshape.reshape import unstack
-> 4577         return unstack(self, level, fill_value)
   4578 
   4579     _shared_docs['melt'] = ("""

/home/nobackup/repo/pandas/pandas/core/reshape/reshape.py in unstack(obj, level, fill_value)
    463     if isinstance(obj, DataFrame):
    464         if isinstance(obj.index, MultiIndex):
--> 465             return _unstack_frame(obj, level, fill_value=fill_value)
    466         else:
    467             return obj.T.stack(dropna=False)

/home/nobackup/repo/pandas/pandas/core/reshape/reshape.py in _unstack_frame(obj, level, fill_value)
    476         unstacker = partial(_Unstacker, index=obj.index,
    477                             level=level, fill_value=fill_value)
--> 478         blocks = obj._data.unstack(unstacker)
    479         klass = type(obj)
    480         return klass(blocks)

/home/nobackup/repo/pandas/pandas/core/internals.py in unstack(self, unstacker_func)
   4374         new_columns = new_columns[columns_mask]
   4375 
-> 4376         bm = BlockManager(new_blocks, [new_columns, new_index])
   4377         return bm
   4378 

/home/nobackup/repo/pandas/pandas/core/internals.py in __init__(self, blocks, axes, do_integrity_check, fastpath)
   3042         self._consolidate_check()
   3043 
-> 3044         self._rebuild_blknos_and_blklocs()
   3045 
   3046     def make_empty(self, axes=None):

/home/nobackup/repo/pandas/pandas/core/internals.py in _rebuild_blknos_and_blklocs(self)
   3134 
   3135         if (new_blknos == -1).any():
-> 3136             raise AssertionError("Gaps in blk ref_locs")
   3137 
   3138         self._blknos = new_blknos

AssertionError: Gaps in blk ref_locs

[toobaz]

The error changes to ValueError: could not broadcast input array from shape (2) into shape (0) if I change cols = ['month', 'year', 'sector'] to cols=slice(None).

[toobaz]

Might be related to #17845 .