Unlike shortcuts, the files in junctions will always show the "fake" path like C:\JunctionFolder\Subfolder\Data even though in reality once you're in C:\JunctionFolder, you are really working in another drive.
Doing a search for files on your C drive will find files in a junction by their fake names C:\JunctionFolder\etc.).
Also, selecting several or all folders in your C drive and opening properties will count the number and size of files in your junction target as well, thus showing more files and total disk usage than what your C drive really contains.
However, the pie chart showin the properties of your drive partition (C) is reliable (right-click C drive, properties) - it will only include data that is written for real. To test this, copy a big file in your junction, and check these properties again.