Bug: Joining MultiIndex with NaNs
#### Code Sample, a copy-pastable example if possible

```python
import numpy as np
import pandas as pd

df1 = pd.DataFrame(data={'col1': [1.1, 1.2]},
                   index=pd.MultiIndex.from_product([['A'], [1.0, 2.0]],
                                                    names=['id1', 'id2']))
df2 = pd.DataFrame(data={'col2': [2.1, 2.2]},
                   index=pd.MultiIndex.from_product([['A'], [np.NaN, 2.0]],
                                                    names=['id1', 'id2']))
print(df1.join(df2))
```
#### Problem description

The index containing the NaN value of `df2` is falsely joined with the index of `df1`. Therefore, the result contains both values of `df2` instead of only one value and a NaN value.

#### Expected Output

```
         col1  col2
id1 id2
A   1.0   1.1   NaN
    2.0   1.2   2.2
```

The expected result was returned by older pandas versions (successfully tested with 0.18.1 ; 0.20.3 ; 0.21.1 ; 0.22.0).

#### Actual Output

```
         col1  col2
id1 id2
A   1.0   1.1   2.1
    2.0   1.2   2.2
```

This result is returned by newer pandas versions, beginning with version 0.23.0 (tested with 0.23.0 ; 0.23.4 ; 0.24.2 ; 0.25.2).

I suppose this is a bug, or am I missing something?

#### Output of ``pd.show_versions()``

<details>

INSTALLED VERSIONS
------------------
commit           : None
python           : 3.7.2.final.0
python-bits      : 64
OS               : Windows
OS-release       : 10
machine          : AMD64
processor        : Intel64 Family 6 Model 94 Stepping 3, GenuineIntel
byteorder        : little
LC_ALL           : None
LANG             : None
LOCALE           : None.None

pandas           : 0.25.2
numpy            : 1.16.2
pytz             : 2018.9
dateutil         : 2.8.0
pip              : 19.0.3
setuptools       : 40.8.0
Cython           : None
pytest           : None
hypothesis       : None
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : None
html5lib         : None
pymysql          : None
psycopg2         : None
jinja2           : None
IPython          : None
pandas_datareader: None
bs4              : None
bottleneck       : None
fastparquet      : None
gcsfs            : None
lxml.etree       : None
matplotlib       : None
numexpr          : None
odfpy            : None
openpyxl         : None
pandas_gbq       : None
pyarrow          : None
pytables         : None
s3fs             : None
scipy            : None
sqlalchemy       : None
tables           : None
xarray           : None
xlrd             : None
xlwt             : None
xlsxwriter       : None
</details>
