Directory permission problems are quite common yes...
I don't think common due to a bug or WordPress problem though, it's generally down to user knowledge and understanding, or hosts that can't configure their servers correctly, the latter being least common..
I've used WP since 2.7, and never had a problem, so i really can't say definitively if there is a common problem in this area, what i can say is it doesn't cause me problems..
In all my time using WordPress i think i've only ever encountered one bug that caused me any problems, and that's now gone after updating to 2.8.. so it's unfair for me to comment conclusively on bugs as a whole..