Ideas
I tested on both mac and pc with new saves in a fresh folder. The mac has never had mods, PC previously had mods but tested without. Lots I tested on were in brindleton bay and forgotten hollow and it occurred on both residential and national park lots.
I did notice that reloading the save didn't always have the same issues. Sometimes it loaded with shelves in tact and no script call fail when placing new shelves, sometimes it loaded with some but not all shelves in inventory with the scrip call error. Tested by opening the save, quitting without saving, and opening again.
I reloaded my initial problem save ~100 times, one of the reloads where the shelves didn't get moved I was able to delete the containment cell and avoid having to redo my shelf setup. I wouldn't really call it a workaround though since only around 5 out of 100 reloads kept the shelves in place.
Placing a lot from the library with both retail shelves and containment cell also had this issue.