I2C Strange Behaviour with RTC and MPU6050
1 k&Omega; pullup to 3.3 V is out of spec.  The maximum required current to drive either line low is 3 mA.

What the heck is C1 doing there!?  That's going to mess up time constants, and couple edges from one line to the other.  I can't even imagine what hallucinations led to doing this.