There's a few things that are probably going on here.
First, the technology used to cloak the plane doesn't look the same as what is used on the Quinjets. They called it "retroreflective shielding" but that's really the wrong term. (That term describes high-visibility things, like road signs, that reflect a lot of light). What it really seemed to be was some kind of active light-refraction system that takes the incoming light from one side of the plane and channels it out the exact opposite point, making the plane "look like" it's background. I don't think this is the same stuff we saw before.
Even if it is the same tech, not that Black Widow only says they can't track the plan -- it's not completely invisible or their "tech boys" wouldn't have seen anything at all.
What's used in Homecoming, it would probably hide the plane from radar (which is just a specific frequency of light), and make it invisible from a distance. But if you got close enough, you would be able to see traces of it: there were parts that weren't covered (the engines, the windows), there would be distortion of the air behind the engines, there'd be distortion around the edges and probably parallax effects if you were close enough, etc. And that's not even counting the noise it would be making.
Also, keep in mind that Toomes had been planning this job for at least a week or so (based on how long Peter was "behaving" in school), and his eager henchman probably much longer. He would have known where the plane was taking off from and where it was going, and probably the route it was taking to get there. That would have been enough information to get him very close to the plane. At that point, the "close-up" effects I mentioned previously would have let him finish the job.