Did they do some of the project without telling me?
Yes, it makes sense. No, you didn't do anything wrong. Write up what you did for your thesis along with the necessary supporting material, but avoid complaining about what the institute did.
I think the key misunderstanding here is that they were giving you an opportunity to interact in a real system and that they might be able to take advantage of what you learned, but made no commitment to do so. The opportunity is the important part.
It may be that they used you as a low cost way to make an exploration. I don't see anything wrong with that.
Had they told you at the beginning that they weren't committed to what you were doing it might have lessened your enthusiasm at the time (as it does now). But, even for their own regular developers they don't make a commitment to accept any particular piece of work, especially before it is attempted.
The purpose of the &quot;exercise&quot; was your education, not their system. You did a good job of that (&quot;productive time to research and develop it&quot;), so you learned some things.
I don't have any advice about the &quot;larger system&quot; as there is too little information.