What is one to do if the wrong Sefer Torah was removed from the Aron:
If the wrong Sefer Torah was removed from the Aron [i.e. not rolled to the right Parsha], some Poskim rule that it is not to be replaced. This applies even if one desires to remove a more Mehudar Sefer Torah, so long as the current one is Kosher. Other Poskim, however, rule it is permitted for the Sefer Torah to be returned and have the correct one removed, due to Tircha Detzibura to have the wrong Sefer Torah rolled to the right place. Practically, one is to be stringent like the first opinion to not replace the Sefer Torah and is rather to open it up and roll it to the correct Parsha. Nevertheless, one who is lenient in a case of Tircha Detzibura does not need to be protested.
Remembered prior to removing from Aron: If one did not yet remove the Sefer Torah from the Aron even though it is already in his hands, it may be exchanged.
Placed Maftir on Bima instead of Rishon: If on a day that one reads from two Sifrei Torah’s [i.e. Shabbos Rosh Chodesh], and one accidentally placed the Maftir Sefer Torah on the Bima instead of the Sefer Torah Torah Rishon, one may nevertheless replace it with the Sefer Torah Rishon.
 Shemesh Tzedaka 31; Mateh Yehuda 282; Erech Hashulchan 144:5; Opinion in Siddur Yaavetz; Sefer Hachaim [Falagi]; Yifei Laleiv 144:2; Kaf Hachaim 144:13; Salmas Chaim 112 in name of Rav Chaim Zonnenfeld; Har Tzevi 1:63; Igros Moshe 2:37; Yabia Omer 8:15-4; Yalkut Kerias Hatorah p. 1368 that so was directive of Rebbe Rayatz; See Piskeiy Teshuvos 144:1
 The reason: In order not to spread a false rumor that the Sefer Torah is Pasul. [Poskim ibid]
 Har Tzevi ibid; Shevet Hakehasi 1:81; Piskeiy Teshuvos ibid
Other opinions: Some Poskim question whether one may replace the Sefer Torah in such a case. [Igros Moshe ibid]
 Zera Yaakov 1, brought in Machazik Bracha 144:1 and Ledavid Emes Kuntrus Achron 1; 2nd opinion in Yaavetz ibid; Ashel Avraham Butchach 144 that by a small Minyan one may be lenient; Igros Moshe ibid that if the Tzibur is Makpid it may be returned
 Conclusion of Kaf Hachaim ibid and Achronim ibid
 Igros Moshe ibid
 Ashel Avraham Butchach ibid; Piskeiy Teshuvos ibid
 P”M 140 M”Z 4 in name of Levush and Elya Raba; Biur Halacha 684:3 “Veim Tah” in name of Achronim; Piskeiy Teshuvos ibid; See however Yalkut Kerias Hatorah p. 1368 that the Rebbe Rayatz once directed to not switch the Sefer Torah in such a case
 The reason: As since in any event one will read from the Maftir Sefer Torah for Maftir, there is no need to worry about a Pegam. [Biur Halacha ibid]