Yes I agree it should be changed. It should be possible to go a bit over on one species if they go the right amount under on another. It's not rocket science.
Easy to fix that. The ports should just keep a note on how much they go over each day, and then as soon as the fisherman have gone over their quota by the equivalent of one day, they get a day off. So they end up with the same amount of fish, but none are wasted and the fisherman get a day off.