I experienced this problem using git 2.17.1; however, from inspection of the next branch, function get_superproject_working_tree() in submodule.c has not changed in 2 years. I believe the problem is related to the fact that when a merge of the submodule reference is in progress, "git --stage —full-name <submodule-relative-path>” returns three seperate entries for the submodule (one for each stage) rather than a single entry; e.g., $ git ls-files --stage --full-name submodule-child-test 160000 dbbd2766fa330fa741ea59bb38689fcc2d283ac5 1 submodule-child-test 160000 f174d1dbfe863a59692c3bdae730a36f2a788c51 2 submodule-child-test 160000 e6178f3a58b958543952e12824aa2106d560f21d 3 submodule-child-test The code in get_superproject_working_tree() uses the “-z” option on ls-files, so it expects null-byte termination between entries. However, the computation of super_sub_len: super_sub_len = sb.buf + sb.len - super_sub - 1; will only work when there is exactly one entry returned. If this line is changed to: super_sub_len = strlen(super_sub); then only the first returned entry is used, and the bug is resolved. strlen() should be safe to use here because strbuf_read ensures the result buffer is null-terminated. Thanks, Sam McKelvie