We don't know how long the Enterprise was at Warp before the core malfunction dropped them out again. The civilian ship could have taken hours to travel to Kronos and hours back again, with the Enterprise right at the edge of Klingon space.
The Mudd ship actually could have taken the longest part of the journey, since we don't get to see the vast majority of the outbound or return journeys for it, which are implied to take quite a while.
I *might* be wrong, but the Enterprise fell out of warp a few hundred thousand km from Kronos. We can see it from where the Enterprise is. Again the warp core malfunction conveniently occurred nanoseconds before they would've dropped out of warp anyway yet it appears to occur in the middle of the trip because no one is prepared for arrival. Surely the Enterprise warping into orbit of Kronos is suicidal but it seems that was the plan? I thought they were going to the neutral zone? Need to see it again (and I will be but not today!!