Strange adapters question before running QIIME2

Hi all! I've encountered a strange result with the quality control analysis.
Using FastQC, it is reported that in a small percentage of the reads (~4-7%) of all samples, there is an adapter sequence (Illumina universal adapter) located in the center of the reads.


What i usually do is merging the paired-end reads using PEAR and then perform the trimming step using fastp. What's weirder is that the adapter sequence changes (Illumina adapter small RNA 3') after the trimming!

Hope you guys can help me find out the reason to this. Thank you!