In my experience they often lack the curiosity to find background information and possess an adequate overview. Like they'll be able to write quite decent code in C++, but in an interview they'll fail at an easy question like 'what are the differences between C, C++, and C#.' (like they'll have no idea about different paradigms)
It's a complacent sort of attitude, like 'I did a degree, so obviously they taught me everything worth knowing.'
The most common I have seen is to obsess over code as an ends in itself. Writing pretty code when the solution doesn't really require it. The other is premature optimization, where all code must be fast, regardless of whether the problem requires it. These both lead to lacking a "get it done" attitude that I've seen in the self-taughts.
It leads me to wonder why we aren't asking, "What skills do school-taught programmers commonly lack?"