I lived in the metro Detroit area for much of my life. This recount has been covered extensively in our local press all week, so the following is my understanding of what happened.
First off, for those not familiar, elections are run and managed by local election boards run by elected officials. In my adult lifetime, every elected office in Detroit has been held by Democrats; generally there are no Republicans even running in the primaries. While blaming Snyder and Schuette may be popular, that is not who caused this to happen.
While mistakes due to human error can and did happen in isolated areas across the state, it was discerning to note that 60% of the Detroit precincts were disqualified from the recount due to election day irregularities. There is a somewhat archaic Michigan law from 1954 that disqualifies a ballot box from being recounted if the totals of recorded votes doesn't match the poll book. Apparently there were a couple of close elections in the early 50's and this law was intended to avoid the potential for ballot box stuffing by corrupt election workers. Unfortunately, that means that simple human error could also disqualify a precinct from being recounted as well. NOTE: this doesn't mean the votes were not counted, it just means that the totals from election night were used in those instances
Why were there specifically so many in a couple areas like Detroit and Flint? While I don't have inside knowledge, from what I have read in the local press, this situation clearly was the result of poorly trained and supervised local election workers.
If the election workers uncover these type of issues, they can be corrected at the end of the night before the boxes are sealed and the numbers reported. In multiple instances, if a machine appears to not accept a ballot, it is re fed into the optical scanning machine. When that happens, the election workers are required to reset the counter, so a vote isn't recorded more than once. In Detroit, that apparently wasn't done, so it appears that some votes were entered multiple times. At the end of the night, these types of issues were known by the election staff, but apparently they either didn't know what to do or just decided it was a long night and they were going home anyway. (If explanations are made at the time, the votes would have been eligible for recount, but none were made and noted) The county Board of Canvassers still certified those same results also knowing that there were these discrepancies before reporting the totals to the state. With Hillary having a lead in pre election polling, and Detroit voting 90% for Democrats, it may have been that a few votes off didn't really matter and it was "close enough" No one anticipated that there would be a recount initiated by Stein. (If anything, Hillary may have received extra votes in the process)
(I worked as a bank teller for a few years. When the numbers didn't balance at the end of the day, no one went home until it was reconciled)
This falls entirely on the backs of the local elected officials in those cities/counties that recruited and trained the election staff in their areas. While most voters pay attention to the candidates running for president, senators & governors, it is all the other down ticket local offices that often get ignored as people often vote of things like name recognition, yard sign proliferation etc. Hopefully this created enough local embarrassment, that the people in charge in Detroit and Flint will address and correct these problems.
Detroit voters in particular have been very poorly served by corrupt/incompetent local politicians. Most recently, former mayor Kwame Kilpatrick (in prison for bribery and corruption), former City Council president Monica Conyers ( just released from prison for bribery) , City council president Charles Pugh ( just convicted of pedophilia) and several others have been forced to resign from office. Not to mention around a dozen school principals all very recently convicted of bribery. Even to go as far as school board member David Murray legally changing his first name to "Reverend" (he is not one) so he would be listed that way on the ballot, which he just won.
(This is not meant to cast any corruption accusations at the people that were in charge for these elections, just pointing out recent history)
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