One, with a fleet, the jump as group doesn't work well, you still get piece meal, but they all wait until they are grouped together before they start jumping, so it isn't as bad as it would be without jump as group (what I mean is that they will all leave the grav well, but not all of them are in a position to charge for a jump before other ships start charging and jumping).
If you're talking about the slightly staggered jump, that was done for the "Star Wars" effect of a mass of ships streaming out of phase space
Another is simply auto-fleet doesn't always work.
There are limits to when auto-fleet join kicks in and when it doesn't, what was the situation?