Actually it happens from time to time. Some clearly wrong decisions about notional times are relatively rare on the top level but with competitors in sub-classes it's unfortunately very common problem.

For example the usual way to give notional time for second runs of stage in FIA events is to allocate competitors the time from first pass of the stage. However they usually do it without taking into account what happened in the first pass. Therefore we had a lot of cases when competitors were given times 3 minutes worse then their competitors because they had a puncture in the first run. It sounds absurd but it happened several times in WRC3 or JWRC in 2014 alone.

In fact it can never be absolutely fair but in my opinion in such situation when the stage is topped for example by WRC2 competitor and all WRC3 and JWRC competitors are affected it's better to give all the same time.