The store content is not causing this, or at least they hadn't been the triggers for many if not most players. The glitch had been noted and dealt with (by the mod) long before the Bohemian Garden and Chicken Coops were made available. The SP mod does run the town for you, but under the player's specifically set guidelines. In other words, it is also a way to manage no or limited forms of progression, it doesn't have to go wild trying to control every aspect of every household in town necessarily.
This page provides a pretty readable overview of how SP works:
http://www.nraas.net/community/StoryProgression-FAQ-General
Many of us deploy some form of Rotational Play by leveraging SP's caste features. If you really do wish to control the entire town, rather than a defined subset of it, to an extent that is also possible by changing the options strategy around a bit to include Active vs. Not Active rather than "in my protected caste or not."
http://www.nraas.net/community/Story-Progression-Rotational-Caste-Settings
If you do wish to pursue these options for progression, that's great but I would suggest bringing more detailed questions about the mod's workings and how best to deploy them to us at NRaas. It's kind of what we are there for. :)