The "control fail" is not a failure of the system but rather a game mechanic itself. If the target that someone is attempting to control has a higher control sub-stat (ex: 10000>5000) than there is a percentage chance that your control fails. The bigger the difference in control the higher the chances that the attempt fails.

In regards to the mysteries that last 2 rounds, they do in fact last the full duration if you are attempting to control a non-naturally immune ninja. Immune ninja's will always reapply their immunity at the start of every round (as that is a part of their kit). As such, most debuffs that suppress-immunity allows to affect the otherwise immune ninja is removed by the start of the next round as their debuff immunity is reapplied and the current debuffs are cleansed. The only exception to this is Edo-Itachi's Dream debuff as it specifically is unremovable without 30 chakra being present during the attempt of removal (though it can only be applied to someone that is not immune to debuffs requiring a prior step before application).