Another cause of "TCP ACKed Unseen" is the number of packets that may get dropped in a capture. If I run an unfiltered capture for all traffic on a busy interface, I will sometimes see a large number of 'dropped' packets after stopping tshark.
On the last capture I did when I saw this, I had 2893204 packets captured, but once I hit Ctrl-C, I got a 87581 packets dropped message. Thats a 3% loss, so when wireshark opens the capture, its likely to be missing packets and report "unseen" packets.
As I mentioned, I captured a really busy interface with no capture filter, so tshark had to sort all packets, when I use a capture filter to remove some of the noise, I no longer get the error.