Positions in cytosine_report did not match the regions in providing bed file

[huichanghuang]

Hi,
I tried to use MethylDackel extract on a dataset aligned with bwameth, and I used -l to provide a bed file.
The command I used is :
MethylDackel extract --cytosine_report --CHG --CHH -l R012V1_Probe.bed -o Nova683-RD-R012V1-200827-LCM-Index100-cap08 hg19.fa Nova683-RD-R012V1-200827-LCM-Index100-cap08.sorted.bam
But it seems the positions in Nova683-RD-R012V1-200827-LCM-Index100-cap08.cytosine_report.txt did not match the regions in providing bed file.
While Bedfile regions be like this:

chr1        27188577        27188687        -
chr1        27188774        27188950        -
chr1        27189076        27189181        -
chr1        27189190        27190183        SFN
chr1        36947992        36948182        CSF3R
chr1        36948190        36948371        CSF3R
chr1        36948380        36948887        CSF3R

The Nova683-RD-R012V1-200827-LCM-Index100-cap08.cytosine_report.txt is:

chr1    27000014        +       0       0       CHH     CTT
chr1    27000018        +       0       0       CHH     CCA
chr1    27000019        +       0       0       CHG     CAG
chr1    27000021        -       0       0       CHG     CTG
chr1    27000022        -       0       0       CHH     CCT
chr1    27000026        +       0       0       CHH     CTA
chr1    27000038        +       0       0       CHH     CTC
chr1    27000040        +       0       0       CHH     CTT
chr1    27000043        +       0       0       CHH     CTT
chr1    27000046        +       0       0       CHH     CCT
chr1    27000047        +       0       0       CHH     CTT
chr1    27000051        +       0       0       CHH     CTT
chr1    27000055        +       0       0       CHH     CCT
chr1    27000056        +       0       0       CHH     CTT
chr1    27000059        +       0       0       CHH     CTT
chr1    27000063        +       0       0       CHH     CTT
chr1    27000067        +       0       0       CHH     CTT
chr1    27000071        +       0       0       CHH     CTT
chr1    27000075        +       0       0       CHH     CTT
chr1    27000079        +       0       0       CHH     CTT
chr1    27000083        +       0       0       CHH     CTT

There are lots of positions beyond my giving regions.
Is that any problem with my command?
Thank you so much! :)