bug.sh

git init bug
cd bug
echo b > a
git add a
git commit -m "first commit"
echo > b
echo -n a >> b
git add b
git commit -m "second commit, first branch"
git checkout HEAD~1
git checkout -b other
echo -n a > b
git add b
git commit -m "second commit, second branch"
git merge-tree HEAD~1 master other
cd ..
rm -rf bug

FWIW, even with the malloc error, the output of merge-tree is still correct and AcidFS still works as expected. You just get a nasty-gram to stderr.