Jesus, what did I start here? :) Only because of these four letters?!
I agree with most of what Tim N and John said (overreaction and common idiomatic expression), a bit more sure instinct or tranquility would have been nice. You can read:
there are constructional flaws, planning errors... shit happened
or
there are constructional flaws, planning errors... shit happened
Just put words in context, and then this common phrase makes totally sense here. That's why it was funny to me that Gigili saw a necessity to remove it. And the meta.stackoverflow threads you linked don't show really a answer (44/43 Votes, and this is even more a idiom than a darn expletive or loud swearing being the topics of those threads)
We imho neither need a rule nor is this a exception of a rule (no vulgar speech or gutter language, no swearing). It's not really worth this whole meta-discussion imho and we will anyway find no compromise.
Instead of a neverending subjective discussion here, I asked on the main site, what this phrase means to most german speakers. It's obvious for english ones when looking at the wikipedia article or movies like Forrest Gump.