OnEntityKill (from the error you posted) is called when an entity is destroyed. This error does not affect anything related to real entities on your server, just as the plugin itself doesn't.
All this plugin does is prevent players from placing new entities if the limit is reached, so it has nothing to do with "TC being deleted and also the entire base decaying."
You should look for the reason elsewhere. Try unloading plugins related to entities, etc.
As for the error itself, I can't reproduce it. In the next version, I will add an additional check to avoid logs, but just to clarify, there is nothing broken on the plugin's part. It seems that you have some sort of plugin that is destroying entities in an unexpected manner.