When you hit your conquest points of 50,000 you should have gotten a pop up similar to when you complete a mission. It's possible it may have been accidentally accepted too quickly especially if it occurred turning in another mission or a completion of a crew skill since they all pop up in the same type of window.
I checked the forums and haven't found any other recent examples of this being reported. If you feel its still an issue you can either submit an in-game ticket if your a subscriber or email your Display Name, Character Name and server to support@swtor.com to verify.
