BUG: Values in pivot table that aren't in original df
### 

- [X] I have checked that this issue has not already been reported.

- [X] I have confirmed this bug exists on the [latest version](https://pandas.pydata.org/docs/whatsnew/index.html) of pandas.

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


### Reproducible Example

```python
import pandas as pd
import numpy as np
df = pd.read_csv('filtered1.csv')


df = df.pivot_table(
    index='X', columns='Y', values='T').reset_index()
df
```


### Issue Description

Some of the values in the pivot table aren't in the file used.  
I attached the file I'm using and a screenshot of my current output
[filtered1.csv](https://github.com/pandas-dev/pandas/files/7540864/filtered1.csv)
![image](https://user-images.githubusercontent.com/64660988/141834814-16324c3e-b80f-44cc-bc06-223100445ab6.png)


### Expected Behavior

I should get a pivot table with only the values in the file.

### Installed Versions

<details>

------------------
commit           : f00ed8f47020034e752baf0250483053340971b0
python           : 3.9.7.final.0
python-bits      : 64
OS               : Linux
OS-release       : 5.15.2-zen1-1-zen
Version          : #1 ZEN SMP PREEMPT Fri, 12 Nov 2021 19:22:07 +0000
machine          : x86_64
processor        : 
byteorder        : little
LC_ALL           : None
LANG             : en_US.UTF-8
LOCALE           : en_US.UTF-8

pandas           : 1.3.0
numpy            : 1.21.0
pytz             : 2021.3
dateutil         : 2.8.2
pip              : 20.3.4
setuptools       : 57.4.0
Cython           : None
pytest           : None
hypothesis       : None
sphinx           : None
blosc            : None
feather          : None
xlsxwriter       : None
lxml.etree       : 4.6.4
html5lib         : 1.1
pymysql          : None
psycopg2         : None
jinja2           : 3.0.3
IPython          : 7.29.0
pandas_datareader: None
bs4              : 4.9.3
bottleneck       : None
fsspec           : None
fastparquet      : None
gcsfs            : None
matplotlib       : 3.4.2
numexpr          : None
odfpy            : None
openpyxl         : 3.0.9
pandas_gbq       : None
pyarrow          : None
pyxlsb           : None
s3fs             : None
scipy            : 1.7.1
sqlalchemy       : 1.4.25
tables           : None
tabulate         : None
xarray           : None
xlrd             : None
xlwt             : None
numba            : None

</details>
