The flares one is not obvious. In addition to the smoke he also duplicated some of the buildings which makes everything look more destroyed as well.
Yes, it the smoke cloning was horribly obvious but I don't really blame the photo editor. One, he can't go about his job with the assumption that his own people are trying to fool him and who knows how many photographs he is having to deal with in how much time.
I really don't think outright photographic manipulation is common because the photographers know that getting caught will ruin their career (and zero tolerance really is the policy, photojournalists have lost their job for simple color correction). What is probably more common is actually staging the photo.
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