We had this issue many times on our trip last week. We had several different anytime FP, regular FP and child swaps. The software was inconsistent with which one was used. We had to go to guest services several times each day to correct mistakes.
For instance, we rope dropped Big Thunder and had an 11 AM FPP. We got a child swap, but when we used it at 10:15 AM, the system used our 11 AM FP instead of the child swap. This left my DD without a FP for our 11 AM ride. Guest services told us that the system is programmed to use FP before child swaps so in our case it opened our FP window early instead of using our swap.
We also had two occasions where half our family was charged anytime FP when we had regular FP available. It was super random.
You also have to watch whenever new anytime FP are added to your account. We had an anytime FP at HS that could work at ToT. We got additional anytime FP after an incident, but in adding these they downgraded our existing FP so they no longer qualified for ToT. I’m sure it was a mistake, but fixing it would have required yet another trip to Guest Relations. It wasn’t worth it for us at that point, but still annoying.