BUG: isin has unexpected behaviour when using a dataframe with a large amount of rows (1.000.001)
- [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.

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

---

**Note**: Please read [this guide](https://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports) detailing how to provide the necessary information for us to reproduce your bug.

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

```python
import pandas as pd
import numpy as np
nans = np.repeat(np.nan, 1_000_001)
big = pd.DataFrame({"test":nans})
assert all(big["test"].isin([np.nan])) == True
 
nans = np.repeat(np.nan, 1_000_000)
small = pd.DataFrame({"test":nans})
assert all(small["test"].isin([np.nan])) == True
assert all(small.dtypes == big.dtypes)
```

#### Problem description
The above code fails on the first assert, but not on the second.


#### Expected Output
The excepted behavior would be that both asserts either fail or succeeds

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

<details>

INSTALLED VERSIONS
------------------
commit           : f2ca0a2665b2d169c97de87b8e778dbed86aea07
python           : 3.7.7.final.0
python-bits      : 64
OS               : Darwin
OS-release       : 19.3.0
Version          : Darwin Kernel Version 19.3.0: Thu Jan  9 20:58:23 PST 2020; root:xnu-6153.81.5~1/RELEASE_X86_64
machine          : x86_64
processor        : i386
byteorder        : little
LC_ALL           : None
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8

pandas           : 1.1.1
numpy            : 1.19.1
pytz             : 2020.1
dateutil         : 2.8.1
pip              : 19.2.3
setuptools       : 41.2.0
Cython           : 0.29.17
pytest           : 5.4.3
hypothesis       : 4.57.1
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : 4.5.2
html5lib         : None
pymysql          : None
psycopg2         : None
jinja2           : 2.11.2
IPython          : 7.16.1
pandas_datareader: None
bs4              : None
bottleneck       : None
fsspec           : None
fastparquet      : None
gcsfs            : None
matplotlib       : 3.3.0
numexpr          : None
odfpy            : None
openpyxl         : None
pandas_gbq       : None
pyarrow          : 0.15.1
pytables         : None
pyxlsb           : None
s3fs             : None
scipy            : 1.5.2
sqlalchemy       : None
tables           : None
tabulate         : None
xarray           : None
xlrd             : None
xlwt             : None
numba            : 0.48.0

</details>
