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aberglas comments on Natural selection defeats the orthogonality thesis - Less Wrong
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One particular example of those "evolutionary accidents / coincidences", is homosexuality in males. Here are two studies claiming that homosexuality in males correlates with fecundity in female maternal relatives:
Ciani, Iemmola, Blecher: Genetic factors increase fecundity in female maternal relatives of bisexual men as in homosexuals.
Iemmola, Ciani: New evidence of genetic factors influencing sexual orientation in men: female fecundity increase in the maternal line.
So, appear to be some genetic factors that prevail, because they make women more fecund. Coincidentally, they also make men homosexual, which is both an obstacle to reproduction and survival (not only due to the homophobia of other's but also STDs. I presume, that especially our (human) genetic material is full of such coincidences, because the lack of them (i.e. the thesis that all genetic factors that prevail in evolutionary processes only lead to higher reproduction and survival rates and nothing else) seems very unlikely.
Interesting point about fecudity.
Perhaps the weakness of evolutionary thought is that it can explain just about anything. In particular organisms are not perfect, and therefor will have features that do not really help them. But mostly they are well adapted.
The reason that homosexuality is an obstacle to survival is not homophobia or STDs, but rather that they simply may not have children. It is the survival of the genes that counts in the long run. But until recently homosexuals tended to suppress their feelings and so married and had children anyway, hence there being little pressure to suppress it.