Electromagnetic interference can wreak havoc with electronics. If stereo wiring is routed anywhere near wiring that leads to that ECU (i.e. just about everything, nowadays), it can induce voltages in the adjacent conductor (acts like a little transformer). Shielding is critical. Even without that, spikes in power demand (caused by the current required to produce each and every big bass thump ...) can overwhelm the vehicle's power supply even if the momentary spike is not long enough to blow the fuse. This can get messy, and it's entirely plausible that the aftermarket stereo could have had something to do with failures in the vehicle's own electronics.
In the VW world, the stock radio is connected to the vehicle's on-board diagnostic CANbus network. Problem is that aftermarket radios use the same wire for something else. Very common for the OBDII port to stop working on a vehicle with an aftermarket stereo, and worse, for a long time (not sure if the issue has been fixed) the VW official dealer scan tool would blow due to a short-to-ground if they merely plugged it in to the OBDII port. Then you get angry posts on the internet wondering why the VW dealer wouldn't do a diagnostic if the vehicle had an aftermarket stereo. Well, guess what, the dealer was right. Aftermarket stereo ... K line connected (supposed to cut the wire, but no way to tell without removing the head unit and tracing wires!!!) ... not only does the OBDII port not work but the scan tool that the dealer used would blow if they merely plugged it in, so they wouldn't do it, and rightly so.