If the .json file was generated with QMK Configurator, congratulations you have stumbled upon a bug. File an issue at qmk_configurator.
If not... how did you miss the big bold message at the top saying not to use other .json files?
If you're referring to having three spots for space bar, the best course of action is to just fill them all with Space. The same can be done for Backspace and Shift keys.
Please double check the other layers of your keymap to make sure there are no random keys present.
We are always accepting customer requests and bug reports. Please file them at qmk_configurator.