How to count entity references from same field in different entity types?
Firstly, create a users view of the format: table with aggregation options with the following fields:
- Company ref.
- Team ref.
- User name.
Then go into the table's settings and add a group and compress function to the first field, and count to the others. Optionally you can use the tally members function and you'll get team names with counts displayed between parenthesis.

Secondly,.. well this is simple but depends on how much you are comfortable with php. 


Create a views_preprocess_view (either that or _views_pre_render) function in your theme or in a custom
module.
Install and enable devel and use dsm() in your function to print the resulting array of your view.
Use entity field query to get a list of your companies.
Compare your views results array with the entity field query results to figure out what is missing from the list.
Add it to the view with 0 or dashes for counts.