BUG: pandas.cut does not give the right answer with nullable integer Series input
#### Code Sample, a copy-pastable example if possible

```python
import numpy
import pandas

input_array = numpy.array([1, 2, numpy.nan, 4, 5])
print('Input array: %s\n' % input_array)

bins = numpy.array([0.5, 2.5, 4.5, 6.5])
print ('Using bins: %s\n' % bins)

test_series = pandas.Series(input_array).astype('Int64')

print('Test series:\n\n%s\n' % test_series)
print('Results of cut:\n\n%s\n'% pandas.cut(test_series, bins))
```

Console output:
````
Input array: [ 1.  2. nan  4.  5.]

Using bins: [0.5 2.5 4.5 6.5]

Test series:

0      1
1      2
2    NaN
3      4
4      5
dtype: Int64

Results of cut:

0    (0.5, 2.5]
1    (0.5, 2.5]
2           NaN
3    (0.5, 2.5]
4    (4.5, 6.5]
dtype: category
Categories (3, interval[float64]): [(0.5, 2.5] < (2.5, 4.5] < (4.5, 6.5]]
````
#### Problem description

`output[3]` should be `(2.5, 4.5]` and not `(0.5, 2.5]` as shown.
Tested in pandas 1.0.0 and 0.25.3.


#### Expected Output
````
Input array: [ 1.  2. nan  4.  5.]

Using bins: [0.5 2.5 4.5 6.5]

Test series:

0      1
1      2
2    NaN
3      4
4      5
dtype: Int64

Results of cut:

0    (0.5, 2.5]
1    (0.5, 2.5]
2           NaN
3    (2.5, 4.5]
4    (4.5, 6.5]
dtype: category
Categories (3, interval[float64]): [(0.5, 2.5] < (2.5, 4.5] < (4.5, 6.5]]
````

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

<details>

INSTALLED VERSIONS
------------------
commit           : None
python           : 3.6.10.final.0
python-bits      : 64
OS               : Linux
OS-release       : 4.4.0-173-generic
machine          : x86_64
processor        : x86_64
byteorder        : little
LC_ALL           : None
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8

pandas           : 1.0.0
numpy            : 1.18.1
pytz             : 2019.3
dateutil         : 2.6.1
pip              : 20.0.2
setuptools       : 40.6.3
Cython           : None
pytest           : None
hypothesis       : None
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : None
html5lib         : None
pymysql          : None
psycopg2         : None
jinja2           : 2.11.1
IPython          : 7.11.1
pandas_datareader: None
bs4              : None
bottleneck       : None
fastparquet      : None
gcsfs            : None
lxml.etree       : None
matplotlib       : None
numexpr          : None
odfpy            : None
openpyxl         : None
pandas_gbq       : None
pyarrow          : None
pytables         : None
pytest           : None
pyxlsb           : None
s3fs             : None
scipy            : None
sqlalchemy       : None
tables           : None
tabulate         : None
xarray           : None
xlrd             : None
xlwt             : None
xlsxwriter       : None
numba            : None

</details>
