I haven't been following the trial closely, but I spent a bit of time skimming through some of the case documents a while back. The government's allegations included a bunch of supporting statements from doctors, who claimed that Theranos frequently gave their patients wildly inaccurate results. It sounds like they weren't able to convince the jury of Holmes' guilt on those charges.
(IIRC, Holmes' lawyers also made the argument that it was not legally possible for her to have committed wire fraud against the patients, because any money that Theranos received would have come from their insurance companies.)
Part of the difficulty is that the empirical data that would have proven how well (or poorly) the technology worked was allegedly stored in a proprietary, bespoke database. When Theranos was ordered to turn over the data to the feds for discovery, they delivered an encrypted copy, and then claimed that the encryption key was lost and the original disk arrays were unrecoverable. Both sides of the case then blamed each other for destroying the last remaining copy of the data, which made for some fun reading.
(IIRC, Holmes' lawyers also made the argument that it was not legally possible for her to have committed wire fraud against the patients, because any money that Theranos received would have come from their insurance companies.)
Part of the difficulty is that the empirical data that would have proven how well (or poorly) the technology worked was allegedly stored in a proprietary, bespoke database. When Theranos was ordered to turn over the data to the feds for discovery, they delivered an encrypted copy, and then claimed that the encryption key was lost and the original disk arrays were unrecoverable. Both sides of the case then blamed each other for destroying the last remaining copy of the data, which made for some fun reading.