I did not have a chance to look at the sugia [subject] in depth, but I did look briefly at Nedarim around pages 5-6 and saw that a neder can forbid speaking to someone. You see this towards the end of the sugia about Shmuel. He says if one says מודרני ממך אסור I am forbidden to you by a neder [vow] he is forbidden. The Gemara there concludes that he would be forbidden if Shmuel holds ידיים שאינן מוכיחות הווין ידיים. [An indication or hint of a neder/vow even if not perfectly clear is  still a neder/vow.] So we see if he would say openly, "I am forbidden to you to talk or do business or sit in your four yards," these all would be forbidden.

So since the laws of herem [excommunication] derive their power from laws of vows, we see that all these things can be forbidden by means of a herem.
So why is the signature of the Gra on the letter of excommunication ignored? Even to the degree that it is thought to be totally irrelevant.

[And you can see in laws of vows that it makes no difference why one person might say to another: "I am forbidden to you under a vow." Since the Gra was qualified to make a decree of excommunication then it is valid for whatever reason he saw to do so.
Furthermore, it seems unlikely to me that it was a mistake.