Reference: https://github.com/Shopkeepers/Shopkeepers/blob/master/src/main/java/com/nisovin/shopkeepers/SKShopkeepersPlugin.java#L411

Currently we spawn the shopkeepers during enable. If there are some protection plugins that have not yet been enabled (eg. GriefPrevention, because we need to enable before them for some of our listeners to properly work), they will not have registered their protection listeners yet. If the bypass-spawn-protection setting is disabled, shopkeepers mobs are expected to not be spawned if some other plugins denies that.

However, this should be a minor issue, since players should be prevented from creating those shops in these areas in the first place (which, however, is not the case currently: #696).
Also related, since this affects shopkeepers which can no longer be spawned: #419