BUG: InvalidIndexError when doing fillna with index that is repeated in df but not in fillna argument
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- [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.

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I get an InvalidIndexError on pandas 1.0.3 when doing fillna to a DataFrame with repeated indexes and using a DataFrame with the same index but without repetitions. I've also tested this use case in pandas 1.1.3 (latest as today)

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

```python
df = pd.DataFrame({"a": 100*(list(range(10))+[None,None,None,None])}).sample(1000, random_state=12).set_index(pd.Series(list(range(100)) * 10, name = "my_index"))
df_fillna = pd.DataFrame({"a": list(range(100))}, index=list(range(100)))
df.fillna(df_fillna)
```

I expect to get a DF with each NaN with index i (there could be more than one) replaced with the unique value in df_fillna with index i but I get an InvalidIndexError.

#### Problem description

The output is an InvalidIndexError.

#### Expected Output

I would expect to replace each NaN with index i (there could be more than one) with the unique value in df_fillna with index i. So, the same as I get when doing this:

```python
df = pd.DataFrame({"a": 100*(list(range(10))+[None,None,None,None])}).sample(1000, random_state=12).set_index(pd.Series(list(range(100)) * 10, name = "my_index"))
df_fillna = pd.DataFrame({"a": list(range(100))*10}, index=list(range(100))*10)
df.fillna(df_fillna)
```

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

<details>

INSTALLED VERSIONS
------------------
commit           : None
python           : 3.7.4.final.0
python-bits      : 64
OS               : Darwin
OS-release       : 19.6.0
machine          : x86_64
processor        : i386
byteorder        : little
LC_ALL           : en_US.UTF-8
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8
pandas           : 1.0.3
numpy            : 1.18.0
pytz             : 2019.3
dateutil         : 2.8.1
pip              : 20.2.3
setuptools       : 39.1.0
Cython           : 0.29.21
pytest           : 6.0.2
hypothesis       : None
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : None
html5lib         : None
pymysql          : 0.9.3
psycopg2         : 2.8.2 (dt dec pq3 ext lo64)
jinja2           : 2.11.2
IPython          : 7.13.0
pandas_datareader: None
bs4              : None
bottleneck       : None
fastparquet      : None
gcsfs            : None
lxml.etree       : None
matplotlib       : 3.3.1
numexpr          : None
odfpy            : None
openpyxl         : None
pandas_gbq       : None
pyarrow          : None
pytables         : None
pytest           : 6.0.2
pyxlsb           : None
s3fs             : None
scipy            : 1.5.2
sqlalchemy       : 1.2.16
tables           : None
tabulate         : 0.8.3
xarray           : None
xlrd             : None
xlwt             : None
xlsxwriter       : None
numba            : 0.51.2

</details>
