According to reports from the NYpost:
"Men in Black 3 has gone on hiatus again, this time for two weeks, after having shut down for a week and started back up. Smith, Barry Sonnenfeld and the producers have been fighting. The start date for filming had already been put off."
According to Sony there is no issues the reason for the delay was not because of an arugument with Smith. A represenative of Sony has stated:
“The only reason production will begin mid-November as opposed to late October is to take advantage of New York State film incentives; suggesting that a disagreement triggered the shift is complete fiction.”
Hopefully things will get back on track. This isn't the first delay that Men In Black 3 has had. But with quick revisions of the script and a two week delay, this gives the actors and the studio more time to give fans the best possible movie of the franchise.