This is a bit obscure, but I worked in the aerospace sector for a few years and this is a real thing. You don't need to understand the science, it's more of an engineering problem.
Whenever an aircraft is grounded there are routine maintenance checks done on it to make sure it's flightworthy for the next journey. During flight, the aircraft's health management and prognosticate systems will be monitoring the various sensors, performance, state and power consumptions of all its systems. If there's a fault (say, a certain sensor in the engine has stopped providing data to the HMAP system) the flight crew will be alerted, and so will ground support, and it will be flagged as an issue to be investigated before the next journey is undertaken. During the next period of downtime, the fault will be sorted out by the maintenance engineers.
Often you'll find that the data provided by the HMAP system is faulty itself, and you get a phenomenon known as No Fault Found, otherwise known as a false positive. It costs the aviation sector millions upon millions each year, and is a real bugbear.
Now, with a bit of handwavium it's perfectly plausible that a group of cyber hackers (or whoever) with the magical item you mentioned could send out a signal that generates an aforementioned false positive. A little extrapolation and you could ground entire fleets this way, because the maintenance guys have to get it fixed before the aircraft is cleared as flightworthy again. So you wouldn't be interfering with the aircraft itself, only it's self-monitoring systems. Thing is about aerospace, they take safety VERY seriously. So that would be my method, and avoids any awkward physics.
Happy to provide more info if you think this could work as a plot device. Hope it helps!