Processing EP, when there is a appeal ongoing already

My previous EP got rejected, and company submit for an appeal.But since I'm not much sure , company submit for an appeal, I went interviews and got another offer, and asked that agency to submit the EP. Anyway the EP got submitted. So I assume my first comany has not made the appeal. but my 2 nd EP also got rejected. Can that get rejected, becasue of the appeal , in the first EP.

An (emplyment) agency cannot apply for an EP, only the employer can.
It is not possible, from the very limited information you gave, to tell why your applications were rejected.