[Edit] Sort of fixed. Settings > Alarms > Reset Alarms fixed the wrong task being marked as done. The task still stays in notification center until I clear it myself though. It'd be nice if it disappeared automatically after you deal with it, like with all the first-party apps.
When I get a notification from 2Do and slide to open 2Do and view the task related to the notification, I get the standard options (snooze, view, okay). When I hit view it goes into the task details screen, but when I mark it as done using the checkmark at the bottom, it either marks a completely different task as done or marks nothing at all. It works fine when I open 2Do myself and go into the details screen. It's only when I hit 'view' via local notifications that I have this problem.
My workaround is to hit 'okay' and mark the task done from there instead of having the app take me into the details screen. This method keeps 2Do's notifications in notification center even after I view them (either manually or from notification center/lock screen) and mark them as completed. I have to clear the notifications from notification center manually, which is annoying. Not sure if 2.6.1 will fix this whenever Apple gets around to approving it, but it's been happening for a while. It just didn't bother me too much until I installed iOS 5.