The Siemens units seem to be following the normal pattern for large, complicated systems. Same thing happens with cars and software.

The early production always has bugs. The designers can't think of everything; life happens. So early production will need more repairs than something that's been around for a while but not yet worn out. For freight units, the first model in a series has lots of bugs; later models have the fixes included from initial production. Passenger units don't get to do that most of the time, since in US practice they tend to be single batches or limited runs of very small batches. So "patches" have to be retrofitted to existing units, rather than relying on replacement with later models.

F59PHI's in Calif had problems initially, at least partially due to their pioneering use of electronic engine control systems (I had several rides behind a freight locomotive on San Joaquins due to engine failures; luckily the F59s had a separate HEP genset). I wouldn't expect much different from the SC-44's. Siemens seems to be trying to fix things, and they do have a good reputation for electrical components (many Siemens inverters used in freight diesels, for instance). And Cal-Amtrak service is hard on equipment, with frequent starts and stops, similar to commuter trains but with longer "cruise" segments. So some "infant mortality" should be expected, and over time will drop off as the weak spots in the design and manufacturing are identified and fixed.

Has EMD never made a bad locomotive? Early SD45s had crankshaft issues. 50 series seemed to be retired early at many railroads. Stuff happens when the design is new or pushes the envelope.