What font are you using, and can you post a screen shot? My guess is this is a ligature. You can turn ligatures off in the Opentype submenu in the Character panel.
It indeed sounds like a random ligature is running rampant, and switching ligatures off ought to temporarily fix it.
But the cause, in my experience, has mostly been that you have two sets of this font installed. Use Find Font to locate where it was installed. Remove that font; usually, InDesign will no longer be able to find it. If it still does, you had two copies active.
Is this happening with all fonts or just one font? Is it happening in all documents or just one? If it is just one font do you have the full font installed or just alternate characters?
I tend to agree with Jongware's answer in terms of the cause, though I've found that turning off ligatures hasn't helped me in the past.
My colleagues and I have had similar problems when two versions of the same font are loaded at once using a font manager such as suitcase. I've had this occur with gillsans and helvetica neue.
If you have access to another machine running IDCC, does the same thing happen when opening the file on the other machine?
If the answer wasn't in my post, perhaps it might be on my blog at colecandoo!
Also, if you are using an open type font (.otf), check Open Type>Discretionary Ligatures in the Character panel or your Paragraph/Character style, which is not the same as Ligatures in the first level flyout
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