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I charge a $50 early check in/late check out fee. I operate on pretty much 100% occupancy, so to give my cleaner time to operate my check out is 10am and check in 5pm. If they want to check in at 11-12 that puts her out and makes her rush. Of course if the space is ready a little bit early I welcome them to come, but I srand strictly by my fee until the day of the reservation.
I would absolutely not let those guests check in at 3am without paying 50% of a night.
I have a 11am check out so a 6am check in could make things a bit crowded.
I have an 11 am checkout too and just an hour ago I had an inquiry from a guest who wanted to check in at 10.30am. Although I’d expect the previous guests to be up and conducting their pre-checkout clean by that time, the bed would certainly be still warm 
Thanks for the info. How would a $50 fee be set for early check-in? I don’t see that option.
Want to thank you for posting this question. I recently had a person send this reques:
" Hey Victoria,
Your place is really nice and I was looking to rent it. I am coming to niagara from Ottawa on friday night(mostly around 12am) with my friends. Can you let me know if it is available for Friday and Saturday Night? Also I have 3 friends with me. Also just wondering if the full apartment is rented or owners are living too?"
20 Aug 2018
My response because I was on the ball due to your question:
"Hello XXX,
Our lower level apartment is currently available for arrival Friday August 24 with check in time after 4 pm until Sunday August 26 with check out by 11:00 am.
If you were looking to come in on Friday August 24th at 12:00 am then that is another night and would need to be booked as Thursday August 23 (Total of 3 nights and not 2 nights).
We live on site as this is our home and live on the upper level…"
Crickets after my response but then I was booked by a lovely group from Atlanta GA a few hours later. I believe I would have missed the 12am reference and or assumed 12 pm - thanks for helping me dodge a bad one!
This is also one of the instances where a Special Offers come in handy.
Just send a special offer including the extra night or extra charge and then send your message saying that they are welcome to book the additional night and that all they need to do is accept your offer.
I had an injury with almost the same request. After explaining that was actually 2 days, I offered a discount for the second day. I would however require a 2 day reservation. They never responded back. Whatever, I don’t want to host someone who is trying to rip me off before they even step into my house.
I also had a weird situation where one guest booked 4 nights, and then asked whether it’s possible to book an additional night 2 days after the first check out. My policy was 2 nights minimum but I still offered them two choices, either book 1 night and pay another cleaning fee, or book 3 more consecutive nights. The second option really just costs a hundred dollars more. They didn’t respond. I sent another follow up and they still didn’t respond. Strange fellows. Thankfully I had strict cancellation policy on and the 48h grace period has lapsed. If they suddenly cancelled their first booking I’ll at least get 50%. Phew.