BUG: DataFrame.groupby drops timedelta column in v1.3.0
- [x] I have checked that this issue has not already been reported.

- [x] I have confirmed this bug exists on the latest version of pandas.

- [x] (optional) I have confirmed this bug exists on the master branch of pandas.

---

#### Code Sample, a copy-pastable example

```python
import pandas as pd
df = pd.DataFrame(
    {
        "duration":[pd.Timedelta(i, unit="days") for i in range(1,6)],
        "value":[1,0,1,2,1]
    }
)

df.groupby("value").sum()
```
results in:
```
Empty DataFrame
Columns: []
Index: [0, 1, 2]

```
The same behaviour occurs whether it's sum, mean, median etc

Note the following gives close to the expected result:
```python
df.groupby("value")["duration"].sum()
```

```
value
0   2 days
1   9 days
2   4 days
Name: duration, dtype: timedelta64[ns]
```

Also, this problem may be unique to Timedeltas as the following similar example, has no problem:
```python
df = pd.DataFrame(
    {
        "duration":[i for i in range(1,6)],
        "value":[1,0,1,2,1]
    }
)

df.groupby("value").sum()
```

gives:

```
       duration
value
0             2
1             9
2             4
```

#### Problem description
In v1.3.0 (and master, commit dad3e7) when performing a groupby operation on a dataframe a timedelta column goes missing.
This behaviour does not occur in pandas 1.2.5


#### Expected Output
The expected output is given by pandas 1.2.5:
```python
      duration
value
0       2 days
1       9 days
2       4 days
```

It is a dataframe, with one column "duration", indexed by the groupby keys

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

<details>

INSTALLED VERSIONS
------------------
commit           : f00ed8f47020034e752baf0250483053340971b0
python           : 3.7.5.final.0
python-bits      : 64
OS               : Windows
OS-release       : 10
Version          : 10.0.19041
machine          : AMD64
processor        : Intel64 Family 6 Model 158 Stepping 10, GenuineIntel
byteorder        : little
LC_ALL           : None
LANG             : None
LOCALE           : None.None

pandas           : 1.3.0
numpy            : 1.21.0
pytz             : 2021.1
dateutil         : 2.8.1
pip              : 19.2.3
setuptools       : 41.2.0
Cython           : None
pytest           : None
hypothesis       : None
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : None
html5lib         : None
pymysql          : None
psycopg2         : None
jinja2           : None
IPython          : None
pandas_datareader: None
bs4              : None
bottleneck       : None
fsspec           : None
fastparquet      : None
gcsfs            : None
matplotlib       : None
numexpr          : None
odfpy            : None
openpyxl         : None
pandas_gbq       : None
pyarrow          : None
pyxlsb           : None
s3fs             : None
scipy            : None
sqlalchemy       : None
tables           : None
tabulate         : None
xarray           : None
xlrd             : None
xlwt             : None
numba            : None

</details>
