It's probably not a bug. They probably just don't have the power to maintain warp. Check the "recharge at warp" statistic in the ship builder. If the number is negative, the ship will lose power while warping. If you have enough fuel cells then that's not a problem, but for longer jumps or ships with few/no fuel cells, they'll drop out of warp when the power runs out. They'll then fly at sublight speed until they have power again, then warp for as long as they can.
The effect can also happen if your ships lose reactors in combat. A ship that loses some but not all power may still be able to move, but doesn't have the power to warp for more than a second or two at a time. If other ships in the fleet are flying in formation with a damaged ship, they'll be stopping regularly to let it catch up.
Additionally, this can happen in some cases where a faster ship is set to escort a slower one. The fast ship will move to the slower one, drop out of warp to not overshoot it, then have to warp again a second later to catch up. You can see it if you use carriers with warp-capable fighters and set them to not recall fighters before warping.
The fleet is all together and the battery is full.