I2C controller used in Keystone SoC has an undocumented peculiarity which
results in SDA-SCL margins being dependent on module clock. Driving high
capacity bus near its limits can result in STOP condition sometimes being
understood as REPEATED-START by slaves (or NACK instead of ACK, etc...).
Driving the module with higher clocks increases the margin between SDA and SCL
transitions, making the operations with higher bus rates more robust. Therefore,
target the module clock to 12MHz instead of 7MHz, still staying within
the specification limits.
Before the change STOP timing looked like this on 400kHz: