HypersomniacLive: Changelog for Update 1.11 (added 29 June 2018):

Battle of Shiloh Confederate version - timer issue fix. In very rare circumstances, depending on speed of time, the battle would follow to the next day, even though you captured Pittsburg Landing.

Please note that you have to secure the objective fully (Green tick will appear) or else the objective will not be considered captured.

HypersomniacLive: I'm not affiliated with the devs or GOG, so the only thing I can do is provide the link to the patch history publicly available on Steam.