Yes, the CDC Moratorium doesn't stop landlords from charging late fees (although some local ordinances do) and it does not wipe out the back rent owed. If you are not paying rent during the Moratorium, you might have a huge rent bill due after December 31, 2020 and then be evicted for non-payment.
For HUD program participants should contact their Housing Authority and report loss of income so rent can be adjusted to meet the current situation. This way, you won't owe a lot of money after the CDC Moratorium ends.
Landlords cannot evict for non-payment of rent until after December 31, 2020 (if the renter meets the requirements and signs a declaration). Before the rent you owe piles up, take action. Contact your landlord and ask to pay back rent on a payment plan or ask your landlord to lower your rent for a few months until you get back on your feet. If you already owe a lot of money, you might want to talk to a lawyer or contact legal aid to get help navigating the eviction laws in your state or city, before the CDC Moratorium ends on December 31, 2020..