First, I did a few of the new secret service missions. All was well, then I got a mission to defend a station (Core Dig) After shooting down a few dozen fighters the mission ended and the mission marker reset to the missing giver's station (the energy cell station.)
After that the mission marker notification kept repeating, that is the yellow mission notification box keeps blinking every few seconds. It also refuses to let me accept any new mission. If I try the new mission enters my log for a second, then the notification box blinks again and my new mission is gone. Same happens when I set a destination through the map or by plotting a course to one of my cap ships.
Second, I bought a capship, the new Argon trader. I sent it to the energy station (same as mentioned above) to pick up 2500 fuel cells. When it arrived it sent out one cargo drone to the station which never came back. I saw in the patch notes:
• Transport drones sometimes take time to reach target (workaround: just wait).
.. so I gave it some time but even several hours later the ship is still waiting. I can't clear it's trading queue either, if I try the trade missions disappears from the list but it will just sit there waiting. If I close and reopen the ship's info window the trade mission is back.
Finally (and least important) it seems like destroyed NPC ships keep spawning drones. I got a kill mission against a cap ship and thanks to the spiffy new radar I noticed it kept launching repair drones, even though I'd already turned it into scrap

All this is in a newly started free play game (2.0, argon merc) without any mods.
I have a savegame in which all three of these problems are visible. If it's helpful I can upload it.