Test case:
echo '(cf.
Foo)' | pandoc -f markdown -t markdown
Output: ( cf. Foo).
A space has been added after the open parenthesis. More precisely, if the native output format is chosen, we see it's a SoftBreak: [Para [Str "(",SoftBreak,Str "cf.\160Foo)"]].
This is a sufficiently rare case that it only occurred once in a 350 page document.