Unexpected intersections produced by bedtools intersect (v2.31.1)

[Bbbbqsh]

Hello,

I encountered an unexpected behavior when using bedtools intersect (version v2.31.1). The command appears to report intersections that should not exist based on the block structure of a BED12 entry.

Command used:

bedtools intersect -wo -s -split -a ./temp/input1.bed -b ./temp/input2.bed

Example input:

input1.bed entry:

chr2    43021276    43281829    cluster_3153    17    -    43021276    43281829    0    2    16,26,    0,260527,

This BED12 entry has two blocks, sized 16 and 26, with block starts at 0 and 260,527.

input2.bed entry:

chr2    43091387    43091494    ENSG00000207087    0    -

Unexpected result

bedtools intersect reports these two entries as intersecting.
However, based on the block structure of the BED12 entry in input1.bed, neither of its blocks overlaps with the interval in input2.bed.