That's not really a "problem".
As explained many times on the forum, vehicles are not aware of each other, because this would surely create an all new class of problems ( traffic deadlocks ). The only way as they *try* to not run into each other, is by starting with a random delay.
Of course, since the path they take is different each time and the delay between them is random, and every gate has a different structure, there always be some occasions when they run into each other. Nothing we can do about it, except increasing the delay between the vehicles, which will of course will cause to have to wait for for them, and won't eliminate the issue entirely.
