If you missed the PDA on your first visit, it is possible that it despawned as part of the level clean-up routine - although I thought quest items were supposed to be protected from despawning, but I could be wrong.
Anyhoo, as long as the spawned PDA was accepted and the mission completed, you should be good to go. You may be stuck with the PDA in your inventory for the rest of the game, but just ignore it and it shouldn't do any harm.
There are no extra patches to download. You are already on the latest 1.1.0019.5 version, which would have incorporated all bug fixes to that point. Unfortunately there are still plenty of bugs to contend with, but we have to accept that the game is still being developed. When the next patch eventually arrives it will undoubtedly include further bug fixes - but probably not for this issue, which (afaik) is not a common one.
Hopefully at some point we will get a sparkling new 64-bit game engine to replace the creaking 32-bit engine that we have inherited, and most of these annoying minor bugs and glitches will disappear.