Hi Teena,
I tried the same in Clarity v13.0, in knowledge store too.You are right. Any new/empty folders also have the PLUS sign next to them which mislead us to think that they have contents in those folders. If you look at the 2nd screenshot, the Templates and Training Materials folders are empty while files only reside in Test Folder, yet i see PLUS beside all the 3 folders!!!!
In the 1st screenshot, we can see the size column showing the filesize against each individual files, but fails to give the sum of all filesizes under a particular folder in the 2nd screenshot, which also would have resolved your concern.
I don't think there is a CA supported way to fix this issue. Why don't you put the same issue as an Idea?
Thanks,
Georgy