I originally raised this bug with libgit2 directly but response was that this is in fact a libgit2sharp error.
libgit2/libgit2#5363

Reproduction steps

Use Repository.RetrieveStatus from libgit2sharp from inside Unity3D editor script.

1. download this: libgit2-git_diff_tree_to_index-Crash.zip
2. download Unity 2019.3.0f5 (other versions crash as well)
3. open the above project
4. select menu item "Git Error/RetrieveStatus - CRASH"
5. note native crash, with the log below

Expected behavior

No crash, instead returns RepositoryStatus

Actual behavior

git2-106a5f2.dll caused an Access Violation (0xc0000005)
  in module git2-106a5f2.dll at 0033:7cb4ae65.

Stack Trace of Crashed Thread 9380:
0x00007FFC7CB4AE65 (git2-106a5f2) git_diff_tree_to_index
0x00007FFC7CBB4B09 (git2-106a5f2) git_status_list_new
0x0000028C392EADBF (LibGit2Sharp) LibGit2Sharp.Core.NativeMethods.git_status_list_new()
0x0000028C392EAB9B (LibGit2Sharp) LibGit2Sharp.Core.Proxy.git_status_list_new()
0x0000028C392E57FB (LibGit2Sharp) LibGit2Sharp.RepositoryStatus..ctor()
0x0000028C392E49FB (LibGit2Sharp) LibGit2Sharp.Repository.RetrieveStatus()

Version of LibGit2Sharp (release number or SHA1)

git2-106a5f2, but also happens with e.g. git2-7ce88e6 (happened with all versions I tried).

Operating system(s) tested; .NET runtime tested

Windows 10