Spells are fairly powerful and their limitations are few, but thus far, one known limitation exists:
For reasons no one has yet been able to discern in-character, while you can do non-mass-preserving alchemy on a chunk of matter (e.g. turn an amount of iron atoms into the same amount of gold atoms), you cannot use mass-preserving alchemy on the exact same matter (e.g. turn the gold atoms back into iron atoms plus additional elements formed out of the excess electrons, neutrons and protons).
The reason this limitation exists is due to tighter Aether tie-in for non-mass-preserving alchemy. You can freely picture this as the atoms being manipulated being ‘captured’ by the Aether (picture a microscopic hug), preventing it from behaving like normal matter in the context of other spells.
This tie-in is irreversible in general. Applying a non-mass-preserving alchemical spell will forever lock that chunk of matter into non-mass-preserving mode. Having too much of this stuff around in general also makes it easier to ‘communicate’ with the Aether and, conversely, for it to ‘‘‘communicate’’’ with you.