we did a 16S RNA analysis using MiSeq kit version 3. This kit makes paired-end reads with a size of 300pb. By merging both reads, we can cover 535 pb of region V3-V5. 

As you can see in the following plot, qualities of reads are really bad after the nucleotid 250. 
Is it normal ?  Perhaps the strategy prefers reads lenghs to the quality ? Did you get something similiar with the same kit ? 

![V3-V5 region][2]
![fastqt quality plot][1]
After merging with Flash 
![After merging][3]


  [1]: https://framapic.org/7luICTwCp8FU/dyD2VMKC7cXW.png
  [2]: https://framapic.org/TASsvk65DaIc/xpkU8WlSSVWX.png
  [3]: https://framapic.org/JNjXjmVbVhHm/1oVAPSZiYRSu.png
As pointed in the comments, Illumina's problems with MiSeq v3 kit and 2x300bp are known and old, see for example [here][1] and [here][2]. Informally, (at least some) Illumina technicians will tell you to stay with 2x250bp, I am not sure if someone at Illumina said so on record.


  [1]: http://blog.mothur.org/2014/09/11/Why-such-a-large-distance-matrix/
  [2]: http://omicsomics.blogspot.com.br/2015/12/loose-2015-threads-1-miseq-2x300-issues.html