Has turbotax changed how it charges for returns because last year I paid for a set amount of returns but now it seems to be a per return charge. Has there been a change?

No. For 2020 there was no change in how the returns were priced. With TurboTax Online you pay per return unless you buy a package like the TurboTax Online Standard 8 Return package. 

With TurboTax CD/Download, you always pay for a package of returns, unless you have run out of returns. Then you can buy single, individually priced returns.

I have two charges on mastercard, 46.00 & 59.80  Wonder if its a mistake?

There is no mistake as you purchased the download standard edition on April 26th, 2024, and then purchased TurboTax Online Deluxe x2 on April 28th, 2024.

Thank you for choosing TurboTax.