Q: Why App Store is charging money even for free applications

It is very possible these charges are what are called "temporary holds" on cards to verify they are valid. The generally disappear within 24 hours. If the charges remain and you cannot explain them, then use the information here to inquire with iTunes support. iTunes Store charges on credit and debit card statements - Apple Support  Apple uses the credit card as part of an identification/authorization procedure.

Then contact iTunes support as I indicated earlier.