Unexpected MISO signals from LSM6DS3
If the SPI chip select signal is low throughout all of the transfers then the LSM6DS3 device will behave as if you are performing a multibyte read (see Figure 10 in the datasheet).  The initial read of the WHO_AM_I register starts the read and the read will continue with subsequent registers while the chip select is low.
The chip select signal must go high to complete the read operation and then low again before starting the operation to write to the control register.