Extremely long check in, constantly...

Liked: It was very clean and the room was spacious. The front desk clerk in the eve was very nice but not very knowledgeable and the morning desk person was very nice and checked us out quickly.
Disliked: I booked on the booking.com app without any problem, had a confirmation number and had called the motel three times over the last two weeks to confirm when we would be arriving l. I even gave them an ETA about two hours before we arrived. And each time we were assured that there would be no problem in checking in as long as it was before 2 AM, and we needed to call them and let them know if we were gonna be later than midnight. I did that and let them know it would be closer to 12:30 AM or 1 AM. And the front desk clerk at that time, once again, assured us that we would have no problem checking in. However, when we arrived at the hotel, the front desk clerk, though very nice, took more than 25 minutes to get us checked in. No other customers were there but us. After 15 minutes of waiting with her having difficulty checking us in on the computer, I asked her to please call and ask somebody for help because we were exhausted and really needed to go to bed I needed to get up early in the morning. It took another 10 or 15 more minutes for her to talk to someone on the phone and get us checked in. There is absolutely no reason why this should?ve been a problem. When it was all over with, she apologized once and explained that it was something to do with the audit being done before that. Again, this could have been avoided, had someone that I spoken to on the several other phone calls that I had made, including herself a few hours earlier, had told us about it and we could have gone to a different hotel. Or, perhaps they could have checked us in over the phone. I don?t know. All I do know is that I asked ahead of time if this would be a problem, was told it would not be, and then we were held up for nearly a half hour for no apparent reason.