Late fee for GSTR9 even if turnover below 2 cr for 17-18

An assessee has 2 GSTINs

Both have turnover below 2cr (1.5cr +1.7 cr=3.2 cr total)

While filing GSTR 9, late fee appears for both even if the turnover is below 2cr.

CBIC vide press release dated 14 March 2020 stated that No Late fees for delayed filing of the Annual Return for the financial year 2017-18 and 2018-19 for taxpayers with aggregate turnover less than Rs. 2 crores.

Here though the aggregate turnover > 2cr, The penalty is calculated twice (for each GSTIN)

Please help!