Transaction regarded twice in statistics

In „transactions per category“ some transactions are counted twice, once under the main category and again in its (correct) sub-category, In some cases I could just delete one of them to correct the statistic. In other cases, however, the cumulative amount for that (main) category ist still too high – with the transaction‘s clone not being viewed anymore so that it can‘t be deleted.
Of course the resulting error is greater for large amounts.