pivot_table(..., values='a')  and  pivot_talbe(...)['a'] yield different output
#### Code Sample

```python
aaa = pd.pivot_table(data=human, index='patient_ID', columns='Hugo_Symbol', fill_value=0, values='RNA.alt.fra')
bbb = pd.pivot_table(data=human, index='patient_ID', columns='Hugo_Symbol', fill_value=0)['RNA.alt.fra']

print(aaa.shape)
>>> (39, 4553)
print(bbb.shape)
>>> (39, 4556)
```
#### Problem description

`pivot_table` with `values='a'` assigned works faster, but in my case, it drop off three columns. 

Any ideas why this is happenning?
Thanks!
