The Ack queues and the download queues may have similar (or even the same) bandwidth restrictions, but they can't have the same name if you want pfSense to differentiate.
To make it easier for me to track, I label all the WAN (i.e. ACK) queues with a qW_ as the prename. I.E. one of them is qW_Nerfed, one is qW_HTTPWEB, one is qW_Games, etc.
My download rules under the LAN all go into a sub queue (so I don't restrict LAN speeds, just actual Internet download speeds) where I have similar rules and traffic restrictions but I label them qSomething. I.E. qNerfed, qHTTPWEB, qGames.
Now I can place my lowest priority into qW_Nerfed/qNerfed. The ruleset is the same (same percentage of bandwidth allowed up and down) but since the names are different, pfSense knows which queue I mean.
You'd think it would be self-evident. If I label a WAN queue qNerfed ad a LAN queue qNerfed, then when I pick the ackqueue/queue it would obviously use the ackqueue "qNerfed" for the first and the queue "qNerfed" for the second. But even though you can create those queues, and label the same in the Traffic Shaper section, it gets confused when you select queues with the same name.
Therefore, just ensure they have different names for the ack queues and queues when creating them in Traffic Shaper.