Do you really think that today snuck up on the ballot counters? Why would this time of night be the proper time to deliver ballots for counting?
It doesn’t make shenanigans, also doesn’t make any sense of any kind.
A couple of fairly sensible logistical explanations spring to mind.
Traffic, a traffic accident for the transport company, a misplaced box of ballots at a poll booth, a lack of staff, a mechanical breakdown with a vehicle, shipping ballots in from overseas military folks and delays at an airport, a software glitch somewhere that required validation of these ballots by hand, postal service issues with mail in ballots holding them up at sorting, etc, etc.
An operation as complicated as voting in an entire state is bound to have some minor hiccups, so not exactly surprising. Voting only closed 6 or so hours ago, so it wouldn't take much delay to have them landing now.
It makes a good story for the tinfoil hat brigade, but a conspiracy this does not make. 'Never attribute to malice that which can be explained by stupidity' and all that. Occam's razor probably has some utility here as well.
Also, let's be real, MI is both pretty solidly R at this point, and ultimately isn't going to matter at this juncture anyway. What possible advantage would sneaky extra ballot boxes gain the Ds (if the implication is that it is the work of the evil D deepstate) at this juncture?
If it was an attempt at influencing the election, it was a pretty poor one...