I don't think there's much you can do.... I had a  federal extension rejected b/c  TP had filed their own previously. I unchecked the EF file of 4868 but the rejection is still there.  

Couple of NJ returns had extensions rejected also due to weird end of season law change that Intuit couldn't keep up with. I filed extensions on state website but couldn't clear the rejection message in EF center. I was able to efile the returns when they got the software updated.

The whole rejection tab is new this year... Intuit will probably clean it up for next year...  It doesn't affect anything.....I wouldn't worry about it.