Disputing credit card charges should not have an effect on your credit score.
According to Experian:
Disputing a charge on your credit card will not negatively affect your
credit standing, although the credit card company may add a statement
to your credit report indicating that the account is currently in
dispute.
Although a dispute notation by itself would not be considered
negative, potential lenders may inquire as to the nature of the
dispute, and some may require that the dispute be resolved before
proceeding with an application for major purchases such as a mortgage.
It is important to talk with your credit card company and be certain
you understand the process for disputing charges on your account, as
well as its policy for how the dispute will be reflected on your
credit reports, if at all.
In some cases, you may be expected to continue to make payments on the
amount in dispute while the charges are being investigated. If so,
failure to make those payments while the investigation is pending
would likely result in your account being reported as delinquent,
which would then negatively affect your credit history and credit
scores. Late payments remain on your credit report for seven years
from the original delinquency date.
I have disputed charges on my credit card before, and I have never had an issue with it affecting my credit score/report. As long as you have proof that your disputes are legitimate (whether that be documents, receipts, etc.), then you should be fine.
