"In one ward there were 9,000 votes cast, 1500 of which were write-ins.
Problem is that only 5,000 voters voted." bb
I don't understand. Do you mean there are only 5,000 voters registered in that ward, and yet 9,000 voters came into the precincts? (That, in itself, might not indicate a problem; at least in Alaska one can vote a 'questioned' ballot outside one's own precinct. For whatever reason, it might be that it was more convenient to vote there that day- I frequently do that; when I am working an election outside my own precinct I vote where I am working.)
Otherwise I don't understand. Was there a controversial issue that encouraged write-in votes?
Or are you saying that there were 'repeat' votes? That a voter- in multiple numbers - voted and then went back repeated times and got another ballot?
That could not legally happen in Alaska. Each voter signs in and then is issued a ballot. Were that voter to reappear, there would be no place for them to sign in.
If/When a system breaks down into outright lawlessness it could be done, with the connivance of the election workers.