Innovus is pretty dumb regarding antenna rules. I have recently worked on a tapeout where it claimed it was antenna clean, but in reality there were 2000 antenna violations. The problem can happen in any wire in any block apparently, but it gets worse if you have partitions (innovus does a bad job when estimating the lengh of the wire that crosses partitions). My advice is too study the violations you got, there usually is a pattern behind. Then try to make innovus avoid/respect the pattern indirectly by enforcing max length/max fanout/max load DRVs.
Good luck.