I 94 expired,i 539 incorrect fee -L2 visa


Need urgent help,I am on L2 visa, spouse on L1A. Our visa is valid for ~4 years and spouse i 94 till dec 2021), due to passport renewal i 94 was only issued for less time. We contacted the employer and requested to apply i 539, but due to the texas storm, they applied just one day before my i 94 expiry. Uscis now sent a rejection notice because of incorrect fee and asking to resubmit with correct fee. My i 94 already expired. As we filed when i was in status(1 day atleast) and also i 539 stated only reg incorrect fee am i good to proceed? And also i am working as i know i am good as i applied for extension, will that be a problem?
My spouse employer is asking to better cross the mexico border and get fresh i 94 as this process will take more time. Planning to travel this week. By any chance will they ask to travel to Home country?
Please help