Yes, something pretty similar has happened to me...so I think you should continue to check back with Disney until things seem "right" to you, and here's why...
Back in December, while we were at BC over Christmas week, I booked a split stay for the same time frame the next year under a bounceback rate. We ended up changing our mind about one of the 2 hotels we'd booked, so I called back a couple of days later while we were still at BC to switch to a new resort -- the Poly. I'd known from the last time I booked a BB rate that you have to pay the equivalent of one night's stay as a deposit, so when the CM told me the new deposit amount I'd have to make for the new Poly reservation, it seemed off...but it was Christmas day, and I'd already spent 45 minutes on hold and/or talking to the CM, so I just figured I was tired and didn't understand, so I trusted the amount she told me I owed, she ran my credit card and said we were booked, and decided not to worry about it. My mistake...
Fast forward to February...we're back at WDW again and decided to switch resorts again, lol -- but this time because I'd learned quite by accident that the room I'd booked at the Poly (a suite) wasn't going to work for us because it didn't have the right configuration of beds for our needs. So once again I called the bounceback line and explained that I wanted to cancel the Poly reservation and book a new one at the CR, but the CM looked and looked and couldn't find the reservation. I looked through my calendar and finally found the reservation number I'd jotted down for the Poly, and guess what? The CM was finally able to find the reservation with the number I'd provided, but it had been cancelled due to lack of sufficient funds for a deposit...without Disney notifying me, and even though they were the ones who told me how much I needed to pay -- it's not like I had a say in it, lol!
I expressed my dismay to the CM on the phone, and he agreed with me that the amount the CM had charged me for the Poly deposit was short by $200ish, but that that should've never happened in the first place, and he had no idea how the CM had made that mistake. He was very apologetic and said that I also certainly should've received some kind of notification that my reservation had been cancelled. Thankfully it didn't negatively impact us since we were switching hotels anyway, but I shuddered to think what would've happened if I'd waited until close to the time of our stay to check on the reservation -- I can imagine we'd be hard pressed to find another room available for Christmas week!
Sorry for the long winded story, lol...but it underscores the fact that Disney unfortunately does make mistakes, and that trusting your instincts is usually the right call. If I had questioned the CM on the "low" Poly balance she said I owed, more than likely the issue would've been resolved then and my reservation wouldn't have ever been cancelled. Hopefully you can get your issue straightened out so you won't have to worry about it anymore.