BUG: Unexpected behaviour of groupby + rank(pct=True, method="dense")
- [x] I have checked that this issue has not already been reported. There was a [previous issue](https://github.com/pandas-dev/pandas/issues/15630) about `rank(pct=True, method="dense")` but it was about applying it to `pd.Series` and has been resolved.

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

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

---


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

```python
import pandas as pd
import numpy as np
data = [
    [1, 3, 1],
    [1, 3, -5],
    [1, 3, 3],
    [1, 3, 3],
    [2, 3, np.nan],
    [1, 3, np.nan],
]
df = pd.DataFrame(data, columns=["gr1", "gr2", "val"])
df["r"] = df.groupby(["gr1", "gr2"])["val"].rank(
    method="dense", pct=True
)
print(df)
```

##### Output:
```
   gr1  gr2  val    r
0    1    3  1.0  1.0
1    1    3 -5.0  0.5
2    1    3  3.0  1.5
3    1    3  3.0  1.5
4    2    3  NaN  NaN
5    1    3  NaN  NaN
```


#### Problem description

The `pct=True` option should always return values in `[0,1]`.  If we remove the row with `gr1==2` there is no issue. Somehow the rank function miscounts the number of elements in each group which should be used to turn the ranked series to `[0,1]` ranked series. Note that `pd.Series([1,-5,3,3,np.nan]).rank(pct=True, method='dense').values` returns the desired output: `array([0.66666667, 0.33333333, 1.        , 1.        ,        nan])` so the issue is related to `groupby`. Also, trying out all the options of `na_option` gives undesired result.

#### Expected Output

```
   gr1  gr2  val         r
0    1    3  1.0  0.666667
1    1    3 -5.0  0.333333
2    1    3  3.0  1.000000
3    1    3  3.0  1.000000
4    2    3  NaN       NaN
5    1    3  NaN       NaN
```

<details>

INSTALLED VERSIONS
------------------
commit           : f2c8480af2f25efdbd803218b9d87980f416563e
python           : 3.9.2.final.0
python-bits      : 64
OS               : Darwin
OS-release       : 20.3.0
Version          : Darwin Kernel Version 20.3.0: Thu Jan 21 00:06:51 PST 2021; root:xnu-7195.81.3~1/RELEASE_ARM64_T8101
machine          : x86_64
processor        : i386
byteorder        : little
LC_ALL           : None
LANG             : None
LOCALE           : None.UTF-8

pandas           : 1.2.3
numpy            : 1.20.1
pytz             : 2021.1
dateutil         : 2.8.1
pip              : 21.0.1
setuptools       : 54.1.2
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>
