"Counter" means to go against. It can be used when two people are offering different arguments on a topic. Or it can be used to discuss when something is working against something else. This phrase means that someone wants to see an end result happen, but the actions that they are taking actually makes it harder to achieve their goal. For example, if someone wants to save money for retirement, but they buy new clothes every time they get a paycheck, that could be counter-productive.

simplifying as much as I can : That you are not just not being productive, but there you are doing the opposite, you are precluding the productivity.