Found mistake in the Torah:
One is required to read from a Kosher Sefer Torah. If an invalidating mistake was found in the Torah, then it is to be closed and a new Sefer Torah is to be brought. One never continues the reading in the invalid Sefer Torah once the mistake is found, unless there is no other Kosher Sefer Torah available. This applies even in Shevi’i. If they already read three verses in that Aliya and are not within three verses from the start or end of a Parsha Setuma/Pesucha, then the Olah is to say the after blessing prior to closing the invalid Sefer Torah. The next Aliya is then continued from the Kosher Sefer Torah, from the area of the mistake. If they did not yet read three verses, or are within three verse of the start or end of a Parsha Pesucha/Setuma, then the after blessing is not to be said on the invalid scroll, and rather a Kosher Sefer Torah is to be removed and one is to read from there the remainder of that Aliya and then say the after blessing. In all cases, all the previous Aliyos read in the invalid Sefer Torah, remain valid.
List of invalidating mistakes: A Pesucha was found in place of a Setuma, or vice versa; A Misspelled word, including if the Kesiv was written as the Keri; A repeated word; A letter that is touching another letter in its entire length, or if it makes it illegible; The leg of a Hei or Kuf is touching its roof; A letter that is touching another letter in its beginning or middle area of writing; A letter that is split in two; Two words written in such close approximation that a child reads it as one word. The letters of a word are so far apart that a child reads it as two words; Mistakes in Chaser and Yasir do not invalidate the Sefer Torah so long as the pronunciation remains the same.
 Michaber 143:4; Ketzos Hashulchan 86:1-4
 Michaber 143:2-4; 2nd opinion in Rama 143:4
 Michaber ibid
 Rama ibid
 Michaber 138:1
 Rama 138:1
 Ketzos Hashulchan 86
 Rama ibid