It sounds like a big misunderstanding and I guess the learning lesson is for you to always to get an invoice from anyone doing work.  

As for the rent from April, we received invoices from OP in mid-April that rents were collected but no payment was ever made.

Warning: This video is GROSS. Do not watch while eating!
After 6 months of non-payment, we were able to perform an eviction for this tenant. The cleaning costs alone were over $9k. In total, including money lost fr...

Document all your efforts, including repair invoices and communications, to show you’re acting in good faith as a landlord.

I did not know of this time log requirement for STRs, so as a newbie I am going back through emails, texts, phone logs, invoices, etc. to determine how much time I spent on everything.  

The only thing that I receive are monthly invoices with fees that they cannot substantiate.

This year I received a bill from the PM with the following line items and costs: - Bathroom 1 : Shower/Tub Caulking | Re-caulk tub- Bathroom 1 : Toilet bolt caps | Missing bolt cap- Bathroom 1 : Window Covering | Missing miniblinds- Bedroom 1: closest to the front door : Door/Knob/Lock | Door know needs tightenedNeeds deadbolt installed- Bedroom 1: closest to the front door : Window Covering | Broken miniblinds needs repaced- Kitchen 1 : Wall/Ceiling | Pull nails and spackle- Living Room 1 : Wall/Ceiling | Nail and holes in paneling- Living Room 1 : Window Covering | Miniblinds need repairedLine ItemsDescription AmountMacomb Glass Invoice $40.99Sherwin Williams Invoice $40.60Walmart Invoice $62.37Total $2,271.271 of 2Ace Hardware Invoice $82.93Ace Hardware Invoice $28.33Ace Hardware Invoice $42.50Macomb Glass Invoice $188.58Walmart Invoice $135.30Ace Hardware Invoice $65.19Ace Hardware Invoice $9.78Shop Supplies $3.00Labour hours 24.18 @$65 rate $1,571.70Total $2,271.27This is a very small, one bedroom apartment in a fourplex. 

They just pay the invoices.

It takes a couple of calls to schedule, then they pay the invoice.

One day several weeks after close, they sent me an "invoice" via email with no body, just an attachment with a jumble of line items - It included one of the two items they were getting a quote for me on (new flooring), some but not all of the items they were supposed to fix as part of the contract (with prices even though they were paying), and a few other items I was not familiar with.