I was scanning stations trying to start the phq mission and found half a dozen (no boron) sparks and messages that show a picture of someone and say "Press A to talk" or something like that but when I press A it engages autopilot or moves the ship and the dialog option disappears. Is this a bug or what?

See if you can find something relevant on Egosoft's forums. Please search there yourself:
http://forum.egosoft.com/viewforum.php?f=180

I have checked but found nothing. I think it is a typo in the new patch, it definitely says press A not F but on the forums it says to press F so I'll try that.

If you have found a bug, they will be very pleased if you report it.

Yes, pressing F instead of A works and now I got my phq. I did find another bug, if you are using an xbox360 game controller and hold down the fire button sometimes it will put you in hyper fast travel mode and shoots you across the sector.

I think I found a way to repair my Phq too, I have assigned it to automatically restock on repair drones and my phq hull is currently at 99% so in a few days if it goes up to 100% I will know it worked.

I don't currently have a egosoft forum account so can't post the bugs. I found another. When your subordinates drop illegal goods by default if puts them in a lockbox which is stupid and it does the same for the player. The subordinates you can select to not put items in a lockbox but for the player there is no such option. That is a major bummer because you soon have an entire sector littered with lockboxes containing illegal goods which npcs don't seem to collect.