Michigan also only counts write in votes for candidates that were pre certified as write in candidates.
There were several from fringe candidates, but from reports I saw from recount observers, there were a sizable number of write in votes for Bernie that were counted as no votes. That also meant that votes for Elvis, Mickey Mouse, Oprah, Kim Kardashian, or Beyoncé were also not recorded as voting for president either.
While not filling in the bubble correctly could be problematic, it isn't correct to say the vast majority of those came from Detroit & Flint. There would be no logical explanation why a particular area of the state would be more predisposed to fill in the ballot incorrectly.
The bigger issue in Detroit was the systemic failure of the City and County election officials. There were 59% of precincts that had errors between the poll books and the tabulated results from the scanners. There were also 95 poll books that were turned in either days later or not at all. These were supposed to be included with the ballots in sealed containers the night of the election. In most instances the numbers were only off by a couple here and there, but there were others that had ballots left in the machines and not turned in. The state is investigating and at this time the issue seems to have been caused by poorly trained and supervised election workers.
http://www.detroitnews.com/story/news/politics/2016/12/15/records-detroit-poll-books-missing-several-days/95476742/
http://www.freep.com/story/news/columnists/rochelle-riley/2016/12/16/riley-supervisor-poll-workers-not-capable-job/95495230/
http://www.detroitnews.com/story/news/politics/2016/12/12/records-many-votes-detroits-precincts/95363314/