A freshly rolled cigar carries traces of ammonia. Tobacco leaves are fermented in pilones, large stacks in the curing barn that heat up under their own weight. Fermentation breaks down sugars, pulls out bitter compounds, and, as a side effect, produces ammonia. Manufacturers ferment carefully and at length precisely to bleed off as much of it as they can before rolling. Some always remains. After rolling, the cigar continues to off-gas slowly for months.
Cigar industry writers describe a sick period in the first months of a cigar’s life during which the ammonia is still off-gassing and the flavours read as muted or closed. The shape of that curve depends on the cigar. By most accounts, the sharp ammoniac smell fades substantially within the first few months, is mostly gone by the end of the first year, and is essentially gone by the second.
Smoke a cigar deep in its sick period and you may, depending on your sensitivity, feel slightly off afterwards. There is nothing wrong with the leaf. There is too much ammonia in the air around your palate.
You cannot tell from a label whether a cigar is in or out of its sick period. You can tell from the nose. A clean, sweet barnyard nose is a cigar ready to smoke. A sharp note that makes you instinctively pull back is a cigar that wants more time.
The longer treatment of ammonia, fermentation, and the off-gassing curve sits in How to Rest a Cigar.