BUG: partial nan levels missing when grouping
from #10468 

```
In [40]: df = DataFrame({'A' : [1,2,3]},index=pd.MultiIndex.from_tuples([(1,np.nan),(1,1),(2,1)],names=['first','second']))

In [41]: df
Out[41]: 
              A
first second   
1     NaN     1
      1       2
2     1       3

In [42]: df.groupby(level='second').sum()
Out[42]: 
        A
second   
1       5

In [43]: df.groupby(level=['first','second']).sum()
Out[43]: 
              A
first second   
1     1       2
2     1       3
```

I suppose that [43] is missing the `(1,nan)` group here.
