Missing or extra letters in the Sefer Torah
Rashi in this week's parsha (Chayei Sarah) comments on the pasuk (25,6) ולבני הפילגשם that פילגשים is written חסר and therefore we learn out that Avraham only had 1 pilegesh Hagar. The only problem is that in our sifrei torah it is actually written ולבני הפילגשים with the extra י (and therefore the drasha does not work). In other words either our sifrei torah have an extra letter or Rashi's is missing one.
This is one of a number places where our sifrei torah differ for either statements of Chazal or Rishonim. R' Akiva Eiger (Shabbos 55a) collects over 20 cases from all over Shas, medrashim, etc. where our mesora differs from either Chazal's or the Rishonim.
The acharonim (see for example Minchas Chinuch on the mitzva of writing a sefer torah, Shaagas Aryeh siman 36, etc.) are very bothered by this and wonder how we can make a beracha nowadays on krias hatorah.