I have noticed transaction fees now even when clients pay an invoice via a Bank Transfer. Is this new?

Yes, you're right, @nicole-nicolejzi. QuickBooks charges a 1% fee for ACH payments, up to $10 per transaction. This low rate benefits small businesses, especially those with high transaction volumes and lower dollar amounts.

I've included a screenshot here with details about the credit card processing fees.

I'm adding some links on how to customize categories and updates to expense categories for your reference:
 

• Custom categories in QuickBooks Self-Employed
• Updates to expense categories in QuickBooks Self-Employed

We're always around if you have additional questions regarding the ACH fee or other related concerns in QuickBooks Self-employed. It's our priority to offer further assistance.

@nicole-nicolejzi 

If you are B2B, you can use a 3rd party processor to accept ACH payments for free. Unfortunately it only supports QBO and you must record it manually in QBSE/QBSP.