If you restart steam after pausing a download, and then another game starts to update, steam will forget how to count.
I believe this is the same (bad) behavior on all platforms.
See this issue https://github.com/ValveSoftware/steam-for-linux/issues/361
Going through old reports, closing this as a duplicate of #361 ;)
If you restart steam after pausing a download, and then another game starts to update, steam will forget how to count.