Indexing broken inside groupby - apply
#### Code Sample, a copy-pastable example if possible

```python
import pandas as pd
import pdb

df = pd.DataFrame(
	{
		'col1': ['A', 'A', 'A', 'B', 'B', 'B'],
		'col2': [1, 2, 3, 4, 5, 6],
	}
)

def fn(x):
	pdb.set_trace()
	x.col2[x.index[-1]] = 0
	return x.col2

result = df.groupby(['col1'], as_index=False).apply(fn)
print(result)

```
#### Problem description
The expected output is:
```
0  0    1
   1    2
   2    0
1  3    4
   4    5
   5    0
```
Instead, I get a Series one row longer than expected:
```
0  0    1
   1    2
   2    0
1  3    4
   4    5
   5    6
   5    0
```
The problem seems to come from processing the second group (col1 == 'B'), where indices do not match row numbers. If I stand at the breakpoint (pdb.set_trace()), I can run this with the following results:
```
-> x.col2[x.index[-1]] = 0
(Pdb) x.col2     
3    4
4    5
5    6
Name: col2, dtype: int64
(Pdb) x.col2[5]
*** KeyError: 5
(Pdb) x.col2[5] = 0
(Pdb) x.col2
3    4
4    5
5    6
5    0
Name: col2, dtype: int64
(Pdb) x.col2[5]
5    6
5    0
Name: col2, dtype: int64
(Pdb) x.col2[5] = 0
(Pdb) x.col2
3    4
4    5
5    0
5    0
Name: col2, dtype: int64
```

#### Expected output
```
0  0    1
   1    2
   2    0
1  3    4
   4    5
   5    0
```
This was working before. Unfortunately, I do not know what Pandas version it was.

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

<details>

[paste the output of ``pd.show_versions()`` here below this line]
INSTALLED VERSIONS
------------------
commit           : None
python           : 3.7.4.final.0
python-bits      : 64
OS               : Linux
OS-release       : 5.5.13-050513-generic
machine          : x86_64
processor        : x86_64
byteorder        : little
LC_ALL           : None
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8

pandas           : 1.0.3
numpy            : 1.17.2
pytz             : 2019.3
dateutil         : 2.8.0
pip              : 19.2.3
setuptools       : 40.6.2
Cython           : 0.29.13
pytest           : 5.2.1
hypothesis       : None
sphinx           : 2.2.0
blosc            : None
feather          : None
xlsxwriter       : 1.2.1
lxml.etree       : 4.4.1
html5lib         : 1.0.1
pymysql          : None
psycopg2         : None
jinja2           : 2.10.3
IPython          : 7.8.0
pandas_datareader: None
bs4              : 4.8.0
bottleneck       : 1.2.1
fastparquet      : None
gcsfs            : None
lxml.etree       : 4.4.1
matplotlib       : 3.1.1
numexpr          : 2.7.0
odfpy            : None
openpyxl         : 3.0.0
pandas_gbq       : None
pyarrow          : None
pytables         : None
pytest           : 5.2.1
pyxlsb           : None
s3fs             : None
scipy            : 1.3.1
sqlalchemy       : 1.3.9
tables           : 3.5.2
tabulate         : None
xarray           : None
xlrd             : 1.2.0
xlwt             : 1.3.0
xlsxwriter       : 1.2.1
numba            : 0.45.1

</details>
