What immediately bugs you when watching an episode? Mine is when they transport someone sitting down and they reintegrate in a standing position (or vice versa). Sure, the tech is near magical but my suspension of disbelief pretty much snaps when they do this.
My biggest thing from the start of tng is just that data is to good. stronger and more damage resistant than worf, smarter than anyone except maybe debatably weasely, all his limitations seem to fall away, virtually immortal. Also the same thing with holograms which became just to overall powerful when they had portable emmitters that they could carry themselves.