this is in beta 009. I've noticed ships getting left behind or stopping along the way when ordered to move orders to other planets. I don't think this happened in earlier versions.

After messing around with this a bit I think I know why this occurs. The situation is the following:
A group of ships is selected.

A move order is issued by right clicking on an unexplored system, or a system that is explored but uninhabited and on which intel is not current (ie no ships in the system).

The ships start moving with 2 commands in queue, Move to (first system on way to target) and Bombard (target system), because right clicking issues the attack order.

Now if the target system is revealed by any means, for example by one of the ships arriving earlier than the others, and the planet is not a suitable target for bombardment, BOTH the order to move and the order to bombard are deleted and any ships that aren't already in phase jumping to the target system just stop.

This only affects capital ships and siege frigates, since the other ships cannot attack colonies and thus will never be ordered to bombard. The fix is not to remove the movement part of the order.