Kosh's ship had to decelerate in order to dock inside the station.
This is a reality of spaceflight...you must both accelerate and
decelerate. Both take time. Especially if you're going to dock. Plus
there was time involved in setting up the docking procedure, turning over
control to Babylon Control, lining up vectors and so on.

The fighters didn't have to worry about any of this. They came
shooting through the gate and barely slowed at all, speeding over to B5
and taking up position.

There have now been several situations in which we've been accused
of "mistakes" that have, instead, simply been things done scientifically
accurately. I have to say (and this isn't directed at you, just more of
a general statement), we're not going to hand everyone everything on a
silver platter, serving up pablum...the nature of a *science fiction*
series is that you should THINK about things. The acceleration/deceleration
thing is one example; some thought about why this would be would have led
to the answer.

And, as evidenced by other messages here, others have taken the time
to look at it from that perspective. Which I think is great.

jms