You may also want to look at the memory occupied by your code on the Arduino. If your code, or one of the libraries you use, is leaking memory or doing dynamic memory allocation, and the code is already occupying a high percentage of available memory, the allocation of memory at runtime can overwrite the program and result in behavior like this.
One way to check this is to run your code on an Arduino compatible device that has more memory such as the MKR1000. If you see that the code behaves correctly on a device with more memory, I believe there is a high chance that your code is overwriting program memory at runtime.