The Indiana Secretary of State’s office has this official vote for President, including write-in totals. However, Jay Parks of the Indiana Green Party has obtained the county-by-county breakdown, and he finds that Marion County, which is easily the most populous county in the state, only reported 2 write-ins. Vigo County, which has Terre Haute, reported zero write-ins. Parks knows of voters in those two counties who voted for Jill Stein but their votes have not been counted.
In response, the state says anyone with any complaints should have complained earlier, and it is now too late to look into the problem. Thanks to Jay Parks for the link and for the information about the problems with the tally.