Let's take water as an example. Say you've got a supply of all the atoms you need and a way to place them precisely enough to reliably get water rather than a mix of hydrogen peroxide and hydrogen gas.
When the atoms combine, they release as much energy as burning hydrogen in oxygen. Equivalent problems for virtually everything.
I'm not sure if it's provably impossible, but AFAIK there is no known way to cool this down fast enough to even be stable for the duration of the TV show's materialisation sequence.
Tea. Earl Gray. Loud.
However, for the specific, fuel cells have a lot of waste heat. And even if they didn't, what you're describing in this situation would cause a mixture of ohmic heating and electrolysis in the water while it's being replicated — you need to get the energy out without the last 10% flash-boiling your tea into steam (or even ice cube or icecream sandwich or whatever).
To rephrase what I said before, it might not be impossible, but AFAIK nobody has a solution yet.
But we can't freeze time, and even if we could I don't see how that would help get rid of the energy of combustion either.
