Last night I went through the game and locked a bunch of shelter entrances against mobile NPCs. This should mean that your prey animals will no longer be able to get into shelters and hide from you. It will have no impact on player-characters' ability to enter these shelters. If you see a prey animal enter a shelter after this, please submit a bug report so that I can fix it (if possible, do it while you're still in the room outside of the shelter--this will make it easier for me to figure out which shelter you were referring to).
In addition, I locked some of the homeplaces in Sted Cair and Lantern Waste against these mobs to prevent the squirrels from sneaking into your house while your doors are unlocked and having a party in there. If this is a problem for you and isn't fixed after today, please submit a bug report about that, too.
Disclaimer: I will not lock up the exits to your favorite RP spot just to keep the mobs from spamming you.