It is not Linux itself but:
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I dislike when something goes wrong with a program and the documentation is not clear on how to fix it. But I do not complain because it is understandable when developers write documentation they have to choose who's hand to hold, if they choose to help everyone then the documentation can get long and perhaps redundant.
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When one is a beginner and installs a distribution for the first time one can get scared by the splash screen showing errors which are 99% of the time safe to ignore (e.g showing that a device was not found). I know its important for developers and advanced users to know all this info but it can make beginners feel so damn scared (like me).
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Naming, like in the general sense, it seems like many software have some ridiculous names (dolphin, ncmpcpp, gimp, foot, gnome). Very subjective, I know, but in the end I love and hate these names.
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Bluetooth... yeah.