This concerns at least zsh, I haven't tried other shells.
Steps to reproduce:
mkdir -p foo/bar
ln -s foo/bar baz
cd baz
cd ../foo
The last command fails with zoxide: no match found.
The problem lies the second if-statement in templates/zsh.txt which uses test -d to check if ../foo is a directory, which dereferences symlinks before expanding ... Therefore ../foo is determined to not be a directory and Zoxide is queried instead of calling the builtin cd. Note that cd works as expected in this scenario.