Plot hole: The shuttle in the opening sequence is flying to the farm, over Jyn's head, directly to the farm, but somehow arrives after she's got home and been hidden in the cave. (00:01:15 - 00:03:15)
Suggested correction: It is common practice for a plane or ship not to immediately land upon first approach to a location, especially in a situation like this with many unknown factors in a possibly hostile environment. The shuttle made its first approach to the home and circled around before finding a place to land some distance away. So yes, it did fly over Jyn's head first, as that was part of it scoping the location before circling around.
Plot hole: Revelations in this film create a potential plot hole in Episode IV, in which Vader says Princess Leia is his only link to learning the location of the Rebel base. In this film, Vader captures the Profundity (Raddus' command ship), which is transporting the Tantive IV in its cargo hold. Vader then watches the Tantive IV fly away with the Death Star plans, leading into the beginning of A New Hope in which he captures that ship. So, the first question is, were there no survivors of the Profundity Vader could interrogate to learn of the location of the Rebel base (assuming the navicomputer has been scrubbed). Even if the entire crew were killed, in A New Hope we see several crewmembers of the Tantive IV have been captured. This film shows that the Tantive IV was at Yavin prior to the battle (evidenced by R2-D2 and C-3PO in the hangar). That then raises the question of why Vader couldn't have interrogated those other crewmembers to learn the location of Yavin as the Rebel base.
Suggested correction: You're forgetting the stakes of the situation. The Death Star plans had just been stolen, and that is Vader's top priority. Even if there were survivors left behind on Raddus' ship, he would not take time to hang back and interrogate them, as he needed to get his forces to immediately chase after the Tantive IV and try to get the plans back before they could be used against the Empire. Then, with the ship captured, Leia is the highest value prisoner to get information from.
