The food drop in season 2 has also been bugging me. It would seem to dsiprove Widmore-Dharma connection, because why would Widome be sending supplies to Island if it was no longer under his control. Also, the Dharma initiative does not seem to exist any more.

Somebody mentined this could be explained by multiple timelines, which gave me a similar idea. What if there aren't multiple timelines, but a single timeline, however the supply drops are from either the past or the future of the same timeline?

It has been shown that the Island moves in time. So supplies send in one time period - eg Dharma in the seventies, could theoreticaly arrive at the Island in different time then the time they originated.

So Widmore could have been connected to Dharma in the past, or will be in the future.