The only way* to fix that problem is for Paradox to develop AI that can perform pattern recognition at near human levels, so it can recognize the front overlap and adjust accordingly, either by shortening or merging the fronts. I wouldn't hold my breath on that one.
That's a bit of an overstatement. On the overlapping fronts question there are probably some "good enough" practical solutions that don't require "pattern recognition at near human levels". Perhaps if two fronts are identical then merge them, perhaps auto merge front lines immediately after naval invasions land. That should cover most cases.