Negative skills cannot be limited down, because if manager goes to the next level evey season and absolute skill value is not improved, then it loses 20% each season.

But there is something much better that can be done and solves the problem.

To set a limit to the difference between skill category (example defense/attack). Example 80%. That means that if defense is 40%, attack can not be more than 120%. If attack is 150%, you won't be able to train attack unless defense goes to 70% (80% diffference). A similar limit can be set as the max difference between a gray and a white skill. Example 160%. So, if some gray skill is -60%, then the maximum for all whites (with limit to 160% in our example) would be 100% (so no train would be available for whites mor than 100%). If that limit is set to 120%, then when a negative is -40%, maximum white becomes 80%!
A 80% can be also the limit between skills of the same color (two grays or two whites).
With this it is not possible to train mutants as well!!!