First things first
Are you playing with 1.04?
Now to the rest
The ships passed the usual jump location just at the border of the gravity well, left the gravity well and started to traverse the void of space in a reincarnation of the Great Trek They did not jump...just kept moving toward the next planet (oviously they didn't get there) I had to order them back to the border of the gravity well and reinstate the order to jump. Then they finally obeyed me and jumped. I took screenshots of the event just so that people would believe me, and I'll upload them when I can.
Do you have a save or replay of this? If you do, send it to firstname.lastname@example.org (only if it happened with 1.04, hence the first question
) and include a description so they can take a look
I haven't seen any normal engine travel for a long time, myself, but it used to be a bug that popped up constantly in beta in different forms
In a second strange occurrence, my fleet (when told to all jump together to a distant planet) split itself up and my one capital ship jumped one totally different way, and the rest jumped together.
I have seen this happen once and only once. Could never figure out how to reproduce it - but I don't know what it is
While mrakomo is right that the fleet now only waits for 90% of its ships to be jump-aligned, they still should not be taking different routes - so it's some bug, but I have no idea what causes it. As the above, if you have a save or replay, send it in