Overrepresented sequences, among other things, might be an indicator of:
- Depending on the pre-processing cleaning might be a something related to an incomplete full elimination of ribosomal RNA
- Presence of adapters (in this case FastQC should detect that)
I suggest to run a quality control before/after the cleaning steps, checking not only on the option "overrepresented sequences" but also other parameters such as "GC content" and "Kmer repetitions" (both provided by FastQC output). This way should give you some details about these sequences. As an option you can also blast them to quickly check what they are.
Once you understand that you can, in my opinion, proceed further.
Have a good day,