Yeah, something went wrong there for sure. The kidnapping is a delayed event that will trigger no matter how many quests you've done or in what order. It works on a timer, basically, and if it occurs within a dungeon it will wait for you to get out before you get a navcom call about the professor being kidnapped (which you didn't get, from my understanding). It then checks for certain conditions, and if, among other things, you found out the spy, then the kidnapping will not take place. I'd have to take a look at one of your earlier saves, preferably after you reported the spy and before the kidnapping occured, before I could figure out what went wrong, as it is probably something very specific.
Technically, the game should handle it if you just go on and rescue the professor from the pirates, and you won't have any game-breaking bugs afterwards. The tunnel will stay open (which is to your advantage, actually), and I'm not sure how the flavor dialog will behave, because now the npcs think you both prevented the kidnapping and rescued the professor, but nothing major beyond that. After all, we designed the expansion in such a way that it can be finished even if you slaughter every living soul in the Black Sea, but that's an extreme example, of course.
Alternatively, you could upload your newest save for my to try and fix it, but with that comes the chance of me messing things up even further.