Late payment on CPT, Tax filing

Hello, I received 3 last late payments for my CPT, I received them in early February. My CPT expired in early December. Currently on F-1 how should I proceed with this, can this be an issue when filing tax next year? Should I return the amount to the employer, so that I don't have any taxable income? Worked for a startup and they use Gusto as HR, so there is no in house HR.