I'm trying to print the attached stl but is not able to print the pattern on top of the 2nd cylinder from right. The few layers right on top is also not fully printed leaving a small gap at the top of the hinge. Is this is hardware limitation (i'm using a 0.5mm nozzle) or my slic3r setting is incorrect? I've tried printing at default setting and lowering layer height to 0.2mm and increasing fill density but results are still the same.

I did not look at the file but from what you said it could be to thin which would require a narrower path. Try setting the nozzle to 0.4

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