I choose point 3. - not too many layers of abstraction but rather a bad abstraction model which, sort of, results in 1. (bad algorithm). Not because an inexperienced programmer did it, but because the architecture makes an efficient algorithm impossible to implement.

The best example that comes to mind is the "n+1 selects" problem in bad ORMs: if your ORM hides the power of SQL joins behind a crappy abstraction, then you need n selects for what could be achieved with one.