Excise tax - two "sets" of late contributions in one year

Employer deposited employee deferrals late in 2023.  One "set" of late contributions was deposited during 2023.  The excise tax associated with this set is below $100.  Another set of deferrals were not deposited until 2026.  The excise tax on that set is over $100.  In reporting on the Form 5330 for 2023, I assume all late deferrals are combined for 2023 and the tax calculated on the total lost earnings, regardless of when the late deferrals were actually corrected (with additional Form 5330s for 2024, 2025 and 2026 for the contributions that were not corrected until 2026).  Employer is filing a VFCP application for the late contributions in 2023.  How do the waiver of excise tax rules (PTE 2002-51) apply for the excise taxes owed for 2023?  Can we view the two sets of late deferrals separately, where the excise taxes on the first "set" can be waived because they are less than $100 and just pay the excise tax on the other set (the tax is over $100 and the correction was well past the 180 day deadline for waiver).  I am inclined to just treat it as one prohibited transaction for the year and pay the entire excise tax owed.  But I am seeing some discussion about only reporting the late deferrals in 2023 that were not corrected until 2026 because the excise tax for the other late deferrals that were corrected in 2023 are waived because they were under $100.  I can't find any legal authority for this position and wanted to see if anyone else has had this issue come up.

The 5330 excise tax form is based on the plan year in which the deposits should have been made timely. 

The amount of taxes are due for a plan year (generally by 7/31 of the plan year following the close of the plan year in which the deposits should have been made).  The excise taxes do for a plan year are based on the lost earnings due for that plan year. 

The excise tax calculation repeats year over year with a separate filing due for each year.  The IRS then reserves the right to calculate additional interest and penalties to be billed subsequently to the filing. 

Use the VFCP calculator.  It will ask for the date of the payroll, the date of deposit and the amount, and to the calculations for you.

you don't provide enough facts but have you looked at utilizing SCC for some of the delinquencies.  Not sure if others agree, but we have looked at those rules and their history and we do not see where it states that only violations post 3/2025 are eligible. The SCC rules focus on how promptly the employer corrected the underlying delinquency and not when the SCC filing occurs.  The effective date language of the final rules don't change that and there is no grandfather/transition rule. If some of the 2023 deferrals were corrected within 180-days of the error then they might be able to fall under SCC.   

As far as your question, the final rules state that you can (should?) treat each pay period separately:  "Generally, the Department has considered each pay period as a separate transaction; however, the Department has permitted more than one pay period to be treated as one transaction under the VFC Program if the pay periods are close together in time and the delinquencies are related to the same cause."  https://thefederalregister.org/documents/2025-00327/voluntary-fiduciary-correction-program?