When they first arrive and Roy gets into the back of the car and pulls down the hatch, there is no condensation on the window and it is clear, but when the camera shifts to the inside view the window is fogged on the outside with the window wiper showing it has been used.
The satellite they track moves east-to-west. While not impossible, nearly all non-polar, low-earth-orbit satellites are launched west-to-east as that leverages the earth's spin in obtaining the necessary orbital speed.
Beyond all the physics holes, the repeated take of an open spinning hard drive to record audio or data is just impossible. A hard drive would be corrupted almost instantaneously if plates are exposed to normal environment, specially in a car like in the movie. Besides there would be no point to do this.
If the object were in low earth orbit, lower than the orbit of the satellite that was visible crossing the sky earlier in the film (which it must be if it was obstructing the view of the satellite), it would move across the sky even faster than that satellite did. At the very least it would move between the first and second tracking images, and It would move visibly after it lit up. Instead, it just hangs there, motionless.
1420.163 is the only frequency the signal and beacon appear on while the scientists are working in the car and it is stressed many times yet at the end, after they get the battery plugged in, the system shows 1420.160 on the screen with the pulsing beacon.
Mike and Roy sit for hours sideways looking at their computers in the car, as comfortably as if they're sitting in office chairs. In reality they would be quite cramped, Roy cross-legged in the back, Mike sitting sideways on the seat. Yet they get in and out of the car smoothly and quickly as if their legs aren't in those positions.
One character is described as the project lead for a satellite system. Someone in his position should be reasonably expected to know what Arecibo is, to know that Arecibo transmitted a binary message to space in 1974, and to understand the concept of the "water hole" in the radio spectrum. Yet he claims ignorance of all these things, mostly so the other characters don't have to break the fourth wall and explain them directly to the viewers.
In the 111th minute it is unexplained why Harry cannot pack the telescope into the trunk of the car, when they have no additional items there than when they first arrived for their investigation.
What are astronomers doing in the middle of the woods? Any good skywatcher would be looking for a clear, preferably treeless hill or mountain on which to set up a telescope.
The last slow 30 minutes or so in the movie, the 2 mayor scientists and an engineer, struggle to get a battery recharged in time to save once in a life project data that can prove first contact with aliens. Yet they decide it is more important to load the the car with their gear first for several minutes and then start a time race that almost kill them.
A silly plot hole. Such smart guys didn't even have a jumper cable they could have connected to the car's battery and alternator to keep the computer running to save the data? In reality, a mobile rig with such an amount of electronics installed inside a car would have had a permanent connection to the car's alternator to run and recharge the system. The same way a car powers all of its factory installed electronics like its lights, radio, fan blower, etc.