Additional Voltage on I2C Bus
In the comments you say that you are using an ATmega32U4 with the standard Arduino Wire library. Pullup resistor value for that MCU is specified as 20 - 50k &ohm;. A value of ~32k would cause the voltage you are seeing.

In twi.c we see:-

void twi_init(void)
{
  ...

  // activate internal pullups for twi.
  digitalWrite(SDA, 1);
  digitalWrite(SCL, 1);


To disable the internal pullups you could comment out those lines in the library code. However then you may have problems with the voltage being too low for reliable operation (ATmega32U4 specifies minimum high level of 0.7 * Vcc, which is 3.5 V at Vcc = 5 V). The proper solution is to use an I2C level shifter circuit like this:-