Denial of FMLA 

No, the fact that your doctor did not send the fax with a cover sheet is not a reason for denying FMLA, and it sounds as if the employer is playing games with you.  On the other hand, are your employer's claiming that they can't be sure that it is a legitimate fax, sent by a legitimate doctor?  In any case, have the doctor send it again, with a cover sheet this time.  If your employer denies your request again, and you continue to believe your request is legitimate and the denial unfair, you should call the Michigan Department of Labor and discuss it with them.