Actually, what you measure is not transmittance, but reflectance. In any way, reflectance higher than 100 % in case of ATR is not possible - can you show us a spectrum? What is your reference measurement? The latter should be taken with the ATR accessory in position, but with an uncovered and clean ATR crystal.

Thomas is correct. However 150% transmittinace is the equivalent of negative absorbance,. What it means in practice is that the ATR element was not clean when you recorded the background. There is/was something on the crystal nt present in your sample. Unless the peaks is CO2 which again is the difference between background and sample spectra.