I see. The code is in a zip file. Others publish their code on Github, then I could make an issue. Even when the code is on Github, some people don't like me for telling that the Wire library is used in the wrong way and keep on doing it wrong 
I don't know if Sparkfun supplies a Wire library with the board. They use their own bootloader, but I don't see a specific Wire library: GitHub - sparkfun/SAMD21_Dev_Breakout: An Arduino shield-compatible breakout board for the ATSAMD21G18. Battery-power enabled, with an onboard LiPo charger..
If the bootloader is compatible with the bootloader of the Arduino M0 or Arduino Zero, then you could select one of the official Arduino boards.
If the internal pullup resistors are enabled, they are weaker than with an Arduino Pro Mini.
Does the MPU-6050 module have pullup resistors on the module ?
Without pullup resistors I would expect other problems then a second byte being 255.
Can you try that short example ? You only have to change the Serial to SerialUSB.
You have to do a few tests to get closer to the problem. It is a weird problem and at the moment there are too many things that might be the cause.