if it is only "certain sketches" then are you 100% sure those sketches are meant for the MKR architecture ?
Done it myself and tried to upload code meant for a completely different board only to be met with an error.
BTW that's an adafruit link, not an ARDUINO one.
Despite the similar names for some boards they are not always the same in reality.
I could not get the examples to compile for a REAL ZERO !