Additional calls to function when using GroupBy.apply with multiple index
#### Code Sample, a copy-pastable example if possible

```python
import pandas as pd
df = pd.DataFrame([[1, 2, 3], [2, 2, 3]], columns=['a', 'b', 'c'])
def t(df):
    print(df)
    print('-' * 10)
    return None

g = df.groupby(by=['a', 'b'])
g.apply(t)
print(g.groups)
g.apply(lambda x:print(x.index))
```
#### Problem description
The function is invoked by 'apply' three times while there are only two groups.

#### Expected Output
The function is only invoked once by 'apply' for each group.
#### Output of ``pd.show_versions()``

<details>

[paste the output of ``pd.show_versions()`` here below this line]
INSTALLED VERSIONS
------------------
commit: None
python: 3.6.2.final.0
python-bits: 64
OS: Linux
OS-release: 4.4.0-119-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_HK.UTF-8
LOCALE: en_HK.UTF-8

pandas: 0.21.0
pytest: 3.2.1
pip: 9.0.1
setuptools: 36.4.0
Cython: None
numpy: 1.14.3
scipy: None
pyarrow: None
xarray: None
IPython: None
sphinx: None
patsy: None
dateutil: 2.7.3
pytz: 2018.4
blosc: None
bottleneck: None
tables: None
numexpr: 2.6.5
feather: None
matplotlib: None
openpyxl: 2.4.9
xlrd: None
xlwt: None
xlsxwriter: None
lxml: None
bs4: None
html5lib: 0.999999999
sqlalchemy: 1.1.15
pymysql: None
psycopg2: 2.7.3.1 (dt dec pq3 ext lo64)
jinja2: 2.9.6
s3fs: None
fastparquet: None
pandas_gbq: None
pandas_datareader: None

</details>
