Board Thread:Lore Discussion/@comment-24098614-20150831231559/@comment-6881629-20150901095752

If your on a PC there are [http://www.nexusmods.com/skyrim/mods/68125/? mods] to stop animals reporting crime and the unofficial patch stops some but not all. You can just dismount Shadowmere well out of sight of the crime location (and hope no chicken is watching), your horse will fast travel with you but won't actually follow you. Sneaking should show if your being watched so its handy even if your not going for a sneak attack.

Apparently if Shadowmere dies in deep water he/she will respawn and wait back at the Sanctuary, so that could be a way of stabling Shadowmere if it gets annoying.