For RNA Seq, it is normal to see a high percentage of sequence duplication level. That is because the inherit nature of the RNA Sequencing is to count the depth of coverage of each gene. If you have a high coverage gene, it is likely you will encounter duplication.

As for exome sequencing, you would prefer a uniform coverage, therefore duplication might be a problem

Edit: Actually someone else has asked a similar question before High Duplication Rate of Mapped In RNA-seq