While the situation is discerning, you do realize that 90% of the precincts that can't be recounted voted overwhelmingly for Hillary in counties that have been controlled by Democrats for decades.
This source fails to mention why these strong blue precincts, would as they claimed, "destroy evidence" in concert with the Republicans to somehow ensure a Trump win.
While the issues are random & sporadic state wide, the overwhelming majority are in just 2 counties, Wayne (Detroit) and Genesee (Flint). While some like to blame the machines, the same machines are used state wide. Elections are conducted n the local level
The issue is most certainly therefore caused by poorly trained or supervised election staff who didn't take due diligence to reconcile the totals before sealing the boxes. When the machine appears to not accept a ballot, they did not follow the procedures to reset the counter, but fed ballots in multiple times thus allowing extra votes. Since this occurred most frequently in counties that voted overwhelmingly for Hillary, this most likely gave Hillary extra votes.
The situation is analogous to bank tellers not being able to balance at the end of the day. They are forced to stay until the issue is reconciled, not decide it is close enough because they want to go home.
The state law has been in effect since 1954 that deems ballot boxes with irregularities are not to be recounted making the original results stand. This situation needs to be fixed moving forward, but to imply it was done intentionally to aid Trump is not in any way reasonable.