Vomiting is actually a fairly common phenomenon but its more common with MDA than with MDMA in my experience.
It is also much more likely to happen if you have caffeine in a pill than with just the chemical itself.
That said, it is well known that MDMA stimulates 5-HT3, the so-called "chemo receptor", which triggers nausea and vomiting. There are drugs that specifically work against this (the -setron drugs, ondansetron aka Zofran is one such drug) but they are rarely prescribed by doctors unless you have a condition that warrants it in which case, you shouldn't be taking drugs anyway.
Antacids are pretty much useless but ginger root capsules have helped some people in the past.
I wouldn't necessarily say its a matter of clean versus cut and more a matter of how much active dosage you end up with. The likelihood of nausea increases as the dose increases just like most other drugs that induce terrible anxiety.