Paired mapped Reads, R1(3'end instead of 5'end) and R2 (5'end instead of 3' end)mapped wrong ends

[WRui]

I first used fastp to remove reads that had length < 35bp and then used bwameth-mem2 to map these fastq files.
After mapping, I only used primary proper mapped reads to analysis the fragment size distribution and found that there are some fragment size lower than 35 bp, which should not happen because I already remove reads that length < 35bp. Then I went back to check the bam files, and found that some paired reads R1 and R2 mapped to wrong ends. Here is one example, this paired reads mapped to the top strand, but the start position of R2 is at the left side of R1, and the insert size is also wrong. How to understand this sitution?

A00738:343:H7W5JDSX3:4:1164:23032:7310:I16+0+0:J16+0+0:U24+0+0+0:V03+0+0+0 147 chr1 6508070 60 139M = 6508194 -15 TTGTGTGTGGGTGGTTGTAATTTGAGAGGAAGTATTAGGTAATGTAGGTGTTGGGTTTTGTTGTTTTTATAGTTAGGTGTATAGTGGGGGTTATTAGTATTGTGGTAGGTAGGAGTAGTTTTTGGATGGGTAATTGGGG :FFFF:FF:FFFF:::FFFF:F,FFFFFF:,,,F:FFFFFFFFFFFFFFFFF::F:,F::FFF,:FFF:FFF:FFF:F:FFFFFFFFFFF:FF:FFFFFF:F:FFFFF:FFFFFF:FFFF:F:FFFFFFFFFFFFFFFF NM:i:0 MD:Z:139 AS:i:139 XS:i:98 RG:Z:LDCT65-c1_cfDNA_R.good YC:Z:GA YD:Z:f

A00738:343:H7W5JDSX3:4:1164:23032:7310:I16+0+0:J16+0+0:U24+0+0+0:V03+0+0+0 99 chr1 6508194 60 138M = 6508070 15 GATGGGTAATTGGGGTTTGTGGTAAGTTGGAGTTTTTGAGAGTATAGGTTTTGGAGGGGGTTTTTTTTGGTTTTGGATTTTTGAAAGATAGGGTTTTGTGGAGTTTTGGGGATTTGTAGTTTTTTTGATAGTTGAGAG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:F:F:FFFFFFFFFFFFF:FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFF,F:FFFFFFFFF:FFFFF NM:i:0 MD:Z:138 AS:i:138 XS:i:123 RG:Z:LDCT65-c1_cfDNA_R.good XA:Z:rchr1,-17026884,138M,5; YC:Z:CT YD:Z:f