At this point, my supervisor did the extraction of the plasmid and yeast transformation himself
He failed too.
That was the point when we considered something might be off.

Lol, classic. A well-established method doesn't work when applied by a student... You roll your eyes...
damn incompetent students, I've got better stuff to do
"Repeat it, please!"
...
"What, it didn't work again?"
Wow, that one really IS incompetent...but he/she looked so nice at first...strange...I'll show them how it works

You do it yourself and it doesn't work.

Whaaaaaat??!?

Happens like every single time.

The person who had built this construct (another student, apparently)...

And that's where your supervisor made the error. Never trust your student. Not even a good one. Those supersticions are there for a reason ;-)

Thanks for participating! Even if I fear it won't be your worst experiment by end-PhD-time, it was for sure a pretty disappointing one - but one that thought you a very important lesson about science too! Don't blindly trust others to work well.