Hi, thanks :) I'm only updating items, recipes, technologies etc., all bot logic is done in base mod https://mods.factorio.com/mod/Companion_Drones from Klonan so I can't change it.
Just to be clear, bots are mining creep only when you mark it for deconstruction using deconstruction planner?
In that case, it is natural behavior as they are trying to deconstruct any entity in range, that is marked for deconstruction. You can easily prevent them from interfering by disabling construction by clicking Companion construction toggle in set of icons/buttons on right side of item bar. It will basically disable all construction works for companions so you can use other bots to gather creep. Then you can enable construction again. You can also use shovel to harvest creep manually and bots wont be able to interfere at all.