My client said she paid a 20% withholding tax when paying our invoice from Japan via wire transfer to our US account. This seems excessive and I haven't had this issue with other clients.

You have to take that up with her bank, but to me does not seem excessive, in fact rather cheap.

Every country withholds tax while making payments nonresidents. So Japan must also be having 20% withholding tax on the type of services provided by you. Your client will give you withholding certificate. On your US tax return you will claim foreign tax credit by filing Form 1116.

Was the invoice related to services and were the services performed in Japan?

The Service was provided outside Japan however the order was placed from Japan the clients law firm to our customer service team in Tokyo.