Solved

Not recieving bonus design points

Changes were made to the system this week which mean the research is more detailed than before (check out the new research dialog on the cars page) and it is applied automatically. This is where the confusion is coming from, nothing is wrong, the points were put on your car already.

But I admit we haven't been clear enough announcing this change, so I'll dedicate a blog to it today and mail it out to everyone in-game. It will explain the changes and how the system works now in detail.