Payment portal says I am late and now has a late fee. (FL)

Hello all! I’m new to renting and this is my first apartment. On April 1st the landlord’s property management company and I did the final walkthrough for the delivery of the keys. During that I also gave them the first and last month’s rent via cashiers checks from TD bank. On April 2nd the gave the portal link where I could submit maintenance request and payment. When I logged in it showed I owed a balance of the rent due- which I figured was weird because first month of as given and shouldn’t be paying until May 1st. I checked again this morning and it now has a late fee. I have promptly emailed the company already and reached out through the portal. I am just confused as to how this could happen- I am a first time renter and don’t want this harming my rental history.