It seems pretty standard to place only 1 pair of pull-up resistors near the master chip, like shown in this diagram from a TI note on I2C.
But I've come across one circuit in my line of work that is incorrectly wired like this:
simulate this circuit – Schematic created using CircuitLab
Both the slave and the master have their own set of pull-ups, with their own voltage sources. This does not work. But if you remove R4 and R3, everything works great... But why would those two extra resistors cause issues? Could it be some timing delay as the bus goes low or high on one end of the communication?
Unfortunately I can't post the entire schematic but the master chip is an MCU and the slave chip is a generic DAC with some registers. Neither chip have internal pull-up resistors.