In an essay I want to enumerate and describe negative aspects of using a popular and working tool. Since such issues are usually overlooked (or even underestimated), I call them negative side effects. Now, I'm looking for a better (preferably single) word/phrase to describe those negative side effects, something other than drawback or disadvantage.
A phenomenon that follows and is caused by some previous phenomenon: upshot-
Do not confuse "Upshot" with "upside," which is exclusively positive.
Though the "up" metaphor may lead you to think of a positive connotation, the word is often used for negative effects.
Disbenefits is a word I have used from time to time, though I was astonished to find that it doesn't appear in all dictionaries so may be office-speak, slang or new and is designated as 'British [English]' in the site linked in this answer
Noun: A disadvantage or loss resulting from something: ‘an environmental disbenefit to the area of Teesside’
If you think these side effects are tricky, or perhaps not particularly obvious from the outset, then colloquially you might say these are 'gotchas'.
Merriam-Webster defines 'gotcha' as, "an unexpected problem or usually unpleasant surprise".
Newcomers often use PHP due to the prevalence of tutorials, but the gotchas can make finishing more complex projects very difficult.
An unintended but inevitable secondary result:
he saw poverty as the by-product of colonial prosperity
Google search: weakness, imperfection, handicap, limitation, trouble, difficulty, problem, complication; hindrance, obstacle, impediment, obstruction, inconvenience, discouragement, deterrent, disadvantage, Any of these should work.