Long story short:
Someone was working next to me and everything "worked" for them, after they left, I just could not reproduce that. The protocol is wrong, other things probably as well. But I have no proof.
I am done with trying, my contract has ended and I did not get a new one (I guess that it might be related to the fact that I am "not able" to use the method). Now I really don't know what I should do, just leave and let it be and look like I am lacking the skills, or pushing the but-it-has-never-worked-before issue (though I should have noticed, the person was working next to me in the same room, but honestly, the work I was doing was so extremely time consuming that I was unable to keep an eye on her, plus she could not speak proper English and would just say "yes, yes, of course" instead of "I don't understand") when I don't have any hard proof?
I hate it, I was working so hard and it was good for nothing (at this point I am actually not sure if I can publish a paper and thus graduate with what I have). I cannot even search for a job properly, because I don't know if I am going to get a Ph.D. or not.