I know almost nothing about TRID, so I can't guess where there might be a data entry error that could cause the APR to be lower than the IR in effect for the first 120 pmts. The increase in IR beginning with pmt. #121 will push the APR higher than the teaser rate, and so will the Prepaid FCs.
Elapsed time is always measured in whole and fractional unit periods which you said are 1 month long. As Randy advises, the time interval that matters most is the period beginning on the date of consummation and ending on the date of the first pmt. Unless this loan is very strange, that interval is probably one month (unit period) plus no more than 30 odd days. The "APR Tool" calculator is designed to assume that there is exactly one unit period of time between pmts. #120 and 121, unless you enter dates or data that tell it otherwise. For example, let's say the loan closed on 11/1 with a first pmt due 12/16. You can enter the dates or do the calendar math in your head and enter the values, but they will be 1 unit period plus 15 odd days. When you add a second pmt stream, the APR Tool prefills the unit period data as 120 whole unit periods plus 15 odd days...which is correct.
Sticking with my example, if you see unit period values that are 1 & 15 and 121 & 15, then the problem lies somewhere in the payment streams or the Amount Financed.