Sorry, my last comment was wrong.  You're obviously talking about `values` for both.  What do you think about 

```python
In [7]: df
Out[7]: 
   A  B
0  1  1
1  0  1
2  1  0
3  0  0

In [8]: other
Out[8]: 
   A  A
0  1  1
1  1  0
2  0  0

in [9]: df.isin(other)
```

`(A, 0)` is clearly True and `(A, 2)` clearly False, but I don't see any way to make sense of `(A, 1)`.