Replicated items are assembled on a molecular level and are identical to the original data sample. Just read Diamond Age by Stephenson - all makes perfect sense.
But still . . . did the computer take a lowest common denominator approach, a la Applebee's/Chili's? It could be a problem. For example, Picard is always all, "Computer, tea, Earl Grey, hot." I happen to drink Earl Grey tea most mornings, and I tell you the difference in flavor between brands is monumental. I suppose the computer might have the data sample for like a million different brands and Captain Picard just went into settings beforehand and selected his personal favorite as default. But if it's just defaulting to, like, Lipton or something you can see the problem. 
These are the uptown problems of a cashless future society. Beats the ---steaming pile of meadow muffin--- outta cancer and aids.
In their future there was no sickness, as in when they said colds were something people got a long time ago. Okay there was some disease (McCoy had arthritis, unless he was joking) but not as much of it in the later series.
With the tea I would think that there was only one type of Earl Grey, why have different brands when there is no money and no brand competition? It would just be the classic one from back when Earl Grey made it.
And in the holodecks the food and drinks would be real.
But why would the water in a lake be replicated when there is no need to drink it?
I think the safety thing in the holodecks is lame, if just any self aware holo-program can override them why are they in place? There should be nothing to override, the safety protocols should be there and that's all there is too it. No real bullets, self aware programs, wild creatures, Klingons, WW2 soldiers running through the ship, problems where if the holodeck is shut off the people in there are dematerialized, etc. Nothing like that. No risk at all with an override by a Captain, alien, program, virus, just nothing. But there would be no plot for the shows then, now would there?
