Nasa & Sector 7 didn't work together, no reason they wouldn't have secrets from each other. Nasa might not have even known that Sector 7 existed - Jon Voight didn't
Plot holes are more to do with stuff like Barricade vanishing in the first film despite being shown on the way to the big battle. Some elements of the Allspark as well.
Some of the other stuff mentioned is more along the lines of subpar writing more than plot holes.
For instance the Dinobots in the new film, not a plot hole so much as a lacking presentation - Metal frozen dinosaurs at the start of the film that look like the Dinobots and never gets revisited is a slight plot hole.
All movies have these little hick ups(I could point out tons in the Star Wars Original Trilogy), but Bay's films do seem to have more than their fair share.
In the end though, it simply doesn't matter to me