I have the same problem and it is sole-crushing in the amount of time it takes to correct the issue. For example, our organization uses Stripe and Square in various ways so our checking account has many deposits from these sources. Unfortunately, Quickbooks automatically assigns all deposits from Square with the same payee and category to ALL SQUARE deposits. The same issue occurs with Stripe, paypal, and other similarly sourced transactions, or any other transaction with similar descriptions.  It takes so much time to fix every transaction and I can't find a way to turn this off.