There is a bug in the system. When I went to activate a completed research item, it only took a portion of the needed costs, and I had to use diamonds to complete the update even though the costs were met. This happened twice! It also happened to two players. The game is not taking the cost units correctly even though they are met.
Be sure that you have the box checked
unchecked that says they can automatically take diamonds to complete anything that you are short on. What likely happened is that you didn't realize you were short on something, and so Inno automatically took the diamonds because you've never gone into your settings to change that button. I wish it weren't set to buy diamonds by default, but we have to live with that. Inno needs to make money, I guess.
The gear setting that Gkyr mentioned is where you find the "confirmation of diamonds" box, or something like that. Make sure it is
UNCHECKED. CHECKED. That will avoid a lot of problems in the future.
Edit: I've just been messaged and told that you have to CHECK the box, not uncheck. But you'll find that box under settings. Make sure you choose to confirm all diamond purchases. Mea Culpa for the incorrect info.