This is very simple: 'the files related to the tests' inherently include the negative controls, in fact from your quote of Vecchiotti it is apparent she thinks so.
(...)
This assumption conflicts with the fact that Vecchiotti actually did ask for
specific files in her mails (as it is evident even from one e-mail that Charlie Wilkes has). And also conflicts with the facts that is documented that Stefanoni indicated specific files (both in court and in her e-mail), as items that could be included in the submissions, or not.
Your assumption also conflicts with other important things that you should take in account, as for Vecchiotti's tasks. Vecchiotti in fact she is paid to research and verify the existence of materials and records. If something is missing from the folder she is provided, she is anyway responsible to point it out and verify its existence. She is not suposed to "assume" things. In other words, the fact that she may
think so does not exonerate her from her duty to verify, as she has to do with any hypotheses she has, her thoughts notwithsanding.
Something else that Vecchiotti also should do, a point which further strengenths the previous one, is take note that Stefanoni declared that the laboratory always performed controls, a declaration which was contained in the file that Vcchiotti used as a legal pape to make other claims.
In addition - and this is another element which is not irreelevant at all - Vecchiotti also should have verified the case file at the prelimiary hearing chanchellery, to see if the negative controls were already there (as the prelimiary judge had recorded). It is evident that she did not do this because when questioned about the negative controls she repeatedely justified herself by refering to things that Stefanoni should
send her. She kept saying that she didn't find them because
they were not sent. Which implies, she only asked to Stefanoni, she didn't go anywhere else to collect material for her research.
But moreover, it is also obvious that Vecchiotti
was not aware about the content of the hearings of Oct. 4 and Oct. 8 2008. She just didn't know that the negative controls were deposited on a hearing. It was obvious from what she said in her questioning that she did not know that the judge ordered further documentation to be deposited, and that such documentation included the negative controls, and that Stefanoni was recorded as she deposited them with the preliminary court. Vecchiotti said that she was hearing this information from the first time from Comodi.
You also should not forget the fact that Vecchiotti failed to record any contradiction between: the transcripts where Stefanoni is recorded saying she deposited the controls (oct 8) or the judge's declaration that they would be put in the case file and when Stefanoni stated she always performed them(oct 8), and tha fact that she may not have found the negativ controls in her researches. Vecchiotti failed to point out such issue in her report, and failed to do so also in her interrogation (until Comodi iformed her that the controls were already in the file).
You also have several other elements against Vecchiotti actually.
For example, in her report she wrote that Stefanoni is nowhere reported to clean her laboratory desk with alcohool, and instead the Oct 4. transcript does report about the cleanings procedures extensively. These omissions are glaring in Vecchiotti's report: it is obvious that she only picks up the "hundreds picograms" quote from the legal paper but she ignores all the rest.
It is also obvious that we have Comodi who says things like "you didn't request them" and "the negative controls are already in the file". You may think that this is not an evidence they are there, but it rises anyway the burden of proof if you want to prove the contrary: you can't just ignore a statement by a magistrate without actually doing anythig to disprove it.