I don't know if anyone is aware of this bug, or whether or not it's old news.
Regrettably, I'm unable to provide screenshots, but even after patch 1.1, Embargo is not properly disabling the phase jump engines of civilian vessels within the gravity well. This only applies to ranks 2 and 3 of Embargo; Rank 1 appears to disable phase jumping properly.
Since I was waiting until patch 1.1 to try out multiplayer, I'm unable to confirm whether or not this bug occurs outside skirmishes.
This bug is not merely cosmetic: civilian vessels freely jump out of the system while under the effects of Embargo, and their tooltip does not show the "Phase Engines Disabled" debuff.
Anyone have any information?