Yes, when you go online with Origin, it will automatically download the patch.
Since you bought it digitally (as did I), it also means that you are not able to revert to an earlier version.
You could try reinstalling the game. There is a small chance that the patch was not applied correctly but I've only read of one other instance of that happening so far.
I have also found that moving save games / restoring them for some reason causes the game to behave erratically. I don't think they ever intended it to happen though quite a bit of people are doing it. Most notably, moving a game from one account to another causes some issues (using someone else's save or a downloaded save file).
Question, did you have Origin running while you played the game offline? I'm finding some people that say that the game saves differently if Origin isn't running. Also, if you ran the game at any time using a cracked EXE file, those saved games will be forever damaged when using the legitimate EXE version. I would assume this is to deter pirating and make it difficult to load/use the DLC.
Last but not least... I found this "fix" online. I've tried to wrap my head around it but the English is pretty broken. Its meants to fix saves for those that have used a modified EXE file. I'm not saying you either did or did not use one, but it may work for you. I'm not willing to troubleshoot the save issue on my end as my saves are currently working and I am unwilling to modify my game files. I had to "-----" out two of the words as they are not appropriate for this forum.
"fix it : first go My Documents / EA Games / Dead Space 3 Take a backup of the file folder to save it in the name of the slot01.sav. Game completely delete and re-install the game before you open the My Documents / EA Games / **** folder, create a folder called into Dead Space 3 here, send a backup of a backup of the game where you play ..... slot01.sav your pain and problems will be eliminated. This problem is due entirely to the game after using a different file consists of -----. Does not work with the original backup file to a different -----."