In all my text editors, when I type either a single or double quote mark for a variable, El Capitan is doing odd things with the text characters immediately after the quote, such as adding a diacritic mark or just deleting the text or putting the quote mark on the other side of the last letter so that it is outside the quotes. It makes writing code very frustrating. I've search through system preferences to see if there was something affecting quotes in El Capitan, but haven't found anything yet. This happens even in the Xcode beta for El Capitan, as well as Sublime Text 3, Atom, Visual Studio Code and even in TextEdit.
Single & Double quotes corrupting text
Have you looked at the keyboard settings on the text tab(autocorrection)?
I ran into quotes being adjusted to be left/right quotes, which broke javascript coding, for instance.