I am also having the erratic retention time in the UPLC MSMS which is used to determine pesticide residues.There is fluctuation in the retention time for all the analytes. For example for one pesticide analyte the retention times are between 9.77-9.81 minute for 6 injections from the same vial and same day, repeatability (100 ppb standard). Oven temperature is controlled.
Before I used to have very slight fluctuation ±0.02 minute in the whole batch of standards and samples. I call the service engineer. He is convincing me that it's normal. The equipment is only one year.