The code is quite a mess to be honest. You need to understand how picking works in Construct!
Once you create/spawn a new Molek instance, it gets automatically picked in all the further actions and sub-events. I outlined all these lines with red - they apply to the created instance only:
So the sub-event #27 will compare the color value of the newly created instance only, not any of the other existing instances! Which means "Or pick Molek instance 2" condition is moot, because the picked scope only contains 1 instance.
If you want to compare other instances in a sub-event, you need to use "Pick all" condition first. But then you will need to pick the newly created instance again to change its color variable.
Can you explain what these particular events 26-27 are supposed to do? And then I may be able to tell you how to fix them.