Just to be clear, you completed the puzzle in that room after the one you got the materials without a problem, right?
I will try to replicate the bug here, so expect this post to be updated in the next 30 minutes (or maybe 2 hours, assuming it's more complex than i think haha).
Thanks for letting me know! And sorry for the trouble.
While i try to replicate the bug, feel free to comment here about any possible extra info or if you made any progress.
Edit: Checked the event, tried to replicate in-game multiple times in different conditions, but i couldn't make it fail. It's apparently working properly.
I will post some spoilers below. Since comments on Itch.io doesn't have a spoiler function, i will edit this post deleting the spoilers after your reply, okay?
About returning to the room you got the materials to take some more, don't worry, you're supposed to do this.
Please reply this post to inform wheter you've used the repair machine previously or not.
Edit: Deleted the paragraphs with spoilers.