Changed my table to this seems to have fixed the issue.

CREATE TABLE IF NOT EXISTS PMProjectServiceEquipment (
    CompanyID INT NOT NULL,
    ProjectID INT NOT NULL,
    ServiceEquipmentID INT NOT NULL,
    PRIMARY KEY(CompanyID, ProjectID, ServiceEquipmentID)
);

Removing the ID auto_increment field I believe was causing an issue because it cannot be set in an insert statement.

Having a primary key of CompanyID, ProjectID, ServiceEquipmentID worked for this instance of my table