I assume you mean that a user did a sign up to the Mendix Platform and then joined your company in the DevPortal?
When a user does a signup, the company he or she is assigned to is based on the user's email domain. If the user's domain is not yet owned by a company in the Mendix Platform, a new company will be created for the user instead. It sounds like in this case, someone with the same email domain as you did a sign up and then joined your company. (Since we expect users to sign up with their corporate email address, this should be a colleague of yours)
If you feel the user should not be part of the company, you are able to deactivate the user account if one of your members has Company Admin rights; is not I'd suggest sending an email to firstname.lastname@example.org to help you resolve this situation.
Edit: If it's indeed somebody who got added on project level, you can follow the steps like Mike suggested. Joining projects is purely on invite basis though, so in that case someone with sufficient rights must have invited this user. If this is not the case, please also contact email@example.com
On your project overview page in the app platform, click on the Team tab (on the same page as your project wall). Next click on the Manage Project Security button on the right hand side of the page. This should show you a list of team members with a button next to each member entitled, "Remove member". Please note, this button is only available to team members with proper permissions, I believe SCRUM Master and Product Owner, not sure what other roles have this permission.