Do you have some settings in Preferences > Auto Correction?
No. Autocorrect is not enabled in my preferences.
Are you using an OpenType font? Or perhaps an old Type 1 font?
Are they changing only when entered, or also in old files that you open up to discover character drops?
If so: what OS are you using, and what language? Have you looked at your keyboard/input method setttings recently?
I think I've stumbled upon the cause, though I haven't had occasion to fully test it with many fonts. (It was happening with a variety of fonts, not just one.) On the Character panel options, "Ligatures" was checked. I must have done this unintentionally when looking at another option. Thanks for the feedback!
Oddly enough, I've disproven my theory already. I opened an InDesign document that I created two months ago - long before this substitution thing began - and my text is changing to ligatures/glyphs in this old document. So far, the fonts affected (that I've noticed!) are Georgia and Times Roman (TrueType) and Copperplate Bold (Postscript).
The first time it happened, the text was fine when I viewed or printed the document, but when I saved it as a PDF/X-4:2008, it changed the text. Now, it is changing the text when I open old documents. I am using Mac OS X 10.8.5, English language, InDesign CS6.
I will check my keyboard settings, though how would these change without me manually and intentionally doing so? I am the only one who uses this computer, e.g., I AM the "graphics department."