Agreement says I owe a fee on properties I buy at trustee sale. Do people actually strike that?

That's a wide net and I've seen wider. Somebody's brokerage got stung by a client who toured for four months then bought at auction, and the fix was to write down every method of acquiring real property they could think of.

Ask to strike it. In fifteen years of buying I've never had an agent walk over a carve-out request, and the ones who bristle have told me something useful. Your lienholder situation isn't a loophole, it's a whole separate business you were doing before you met her.

Strike it and put the substitute in yourself. Mine reads roughly: compensation is due on properties Broker introduced to Buyer in writing, or on which Broker performed showing, negotiation, or contract services. Then I add an exclusion list, and it names my existing note collateral by loan number and it names anything acquired at a public sale where the agent had no involvement.

Where I'd disagree with @orchard slightly: the agent isn't the problem, the brokerage compliance person is, and they sometimes can't modify a form without a manager's sign-off. Give her two weeks and don't read the delay as resistance.

The credit bid question is what would bother me. Three percent of what number, exactly? If a clause creates an obligation and nobody can tell you the amount, the clause isn't finished. I'd ask her point blank what her brokerage thinks the fee would be if you took title at sale on your own note. Watching someone try to answer that is usually enough to get the sentence deleted.

Three separate things in your post and they don't have the same kind of answer.

The breadth of that clause is a drafting choice, not a legal requirement. Since August 2024 the written buyer-broker agreement became mandatory in practice for MLS-participating brokerages, and the compensation section is where each brokerage decided how much protection it wanted. Wide language covering assignments and foreclosure sales appears in some forms because agents lost fees to buyers routing around them. Whether that clause is enforceable against you in a given fact pattern depends on your state's law and on how the agreement defines the compensation base, and that is a question for a real estate attorney in your state, not a forum reading.

The request to carve out your existing note collateral is ordinary. You had those liens before the engagement, the agent contributes nothing to a trustee sale where you bid your own debt, and there is no service to compensate. Identify the specific loans in an exclusion schedule attached to the agreement so it doesn't turn into an argument about intent later.

On the accounting question, whether a broker fee paid in connection with taking title is added to your basis in the property or expensed depends on the facts of the transaction, and your CPA has to make that call.

The assumption doing most of the work in your post is that the fee has a defined base. Read the compensation section again and find the words that set the number. If it says purchase price and there is no purchase price at a credit bid, the clause is broken as applied to you, and that is the cleanest argument for striking it.