What is the ruling on money that was deposited into my account as a bonus, knowing that my employer thought it was a bonus for external parties, and not for me?

If the work that was done and for which a reward was received is not part of the assigned duties, then there is no harm in benefiting from the reward. However, if the work is part of your official duties for which you receive a salary, and the reward was given based on the assumption that the person who performed it is not an employee of the giver, then it is not permissible to take the reward unless the employer is informed of the truth and agrees to let you keep it. Otherwise, it must be returned to them.