Its really hard to debug hardware remotely, but I can say that the pins on these boards have proven to be fairly resilient. For instance, there is a guy in this thread ( Connecting MCP2515 via SPI for CAN driver with Android kernel 4.9 ) who hit his SPI pins with 5v, and it apparently survived. Note however that he seems to have only hit it with logic 5v, which would be current limited to whatever the logic port of the 5v device can drive it with, which is probably pretty low. If you hit it with the 5v power supply line, that could be very different.
I have seen the “lost arbitration” error message from the i2c bus on one of mine before. It happens when I plug in a GT911 touchscreen, which works for a little while, but eventually gives me that error. I have no idea what happens that triggers the error, all I know about it is that the i2c bus will be dead until the board is rebooted. Also note that the GT911 is on the 3.3v side of a level shifter, with another i2c device. The other i2c device alone doesn’t cause any trouble, and neither do the 4 1.8v devices.
I wonder if your scope might be interfering with it? Maybe try adding external pull-up resistor and see if that helps? I’d suggest starting with 4.7k.