That's very weird but I wouldn't worry too much. Luckily it's easy for you to take it in for a fix.
If the barrel had twisted in the receiver the bolt wouldn't have been able to engage the receiver. As long as there is no weird wear on the op rod it probably stayed where is was suppsed to be. Once the barrel is installed the pin isn't really doing anything anyway. It's just to line it up during install.
Good luck and don't let it worry you, it's an easy fix.
If the rifle isn't having problems extracting I wouldn't worry about it.
