There was a major bug in version 1.3.4 of CITE-seq-Count. The results were in read counts and not in UMI counts.
This is fixed in version 1.4.0 or above. Please rerun your data as this might provide a cleaner result for your data.
Here is the website referencing the wetlab protocols needed https://cite-seq.com/
pip install CITE-seq-Count==1.4.4
The official documentation can be found here