It can happen. Someone gets confused and thinks it’s a special Shabbos. Or, there is to be an extra layning in an adjoining room because of chiyuvim. So, out come the Sifrei Torah, everyone gathers and kisses them and they go to the Bimah. Before layning, it dawns on the Gabbay, that they have taken out an extra Sefer Torah.
Option 1: Take the Sefer Torah back to the Aron HaKodesh.
Problem: One is shaming the second Sefer Torah
Option 2: Use the second Sefer to read the Maftir, so that it is at least used
Problem: It will need an extra Hagba and Gelila and that is a Tircha D’Tzibura
The above scenario occurred in the Shule I daven at. At the time, they followed option 1, but I was uncomfortable with it because I knew in the recesses of my mind that you don’t return a Sefer Torah like that.
I asked Mori V’Rabbi Rav Schachter what he would have done. His answer was
a) Do not return the second sefer torah
b) Leave it on the Bimah during layning
c) Announce to all, that the second sefer torah was taken out by accident
He didn’t like my Option 2, because it may look like the first sefer torah was Pasul.