Well, there's not much to tell. Prior to our move to SQL Geometry at 10.1, I found that for certain utilities feature classes like hydrants, there would be from time to time more rows in the business table than in the feature (f) table. I discovered that nugget as I was transforming data into Intergraph format via FME.
I didn't even think it was possible to create or otherwise load rows into a feature class using standard ArcGIS front-end methods and not create geometry, but it happened. So it's not a primary key error per say, it's more of a key-constraint violation I would guess.
What I suspect had happened is that hydrants data, coming in from an xy event table created from a spreadsheet perhaps had inverted x,y's or were perhaps in a differenent coordinate system, or had differenent units. But because we use well-defined x,y domains, resolution and tolerances I think the information was added to the A and F table but upon, reconcile, post and/or compress, the invalid values in the F table were dropped, but the business rows remained. That's my theory.