I saw the following behaviour of BEDtools multiinter, which is not really what I expected.

cat test1.bed
chr1    1    6
chr1    6    10
#
cat test2.bed
chr2    6    10
#
bedtools multiinter -i *.bed
chr1    1   10  1   1   1   0
chr2    6   10  1   2   0   1

=> Why does the command concatenates the non-overlapping intervals of test1? Splitting test1 into two BEDs and using BEDtools intersect shown no intersection, as it should be. Any ideas how to circumvent this in multiinter?