Three days out is late, and the frustration makes sense. To answer the first part: this sits squarely with a real estate attorney, specifically one who handles transactional work and entity structuring. A title attorney (sometimes called a closing attorney) handles the mechanics of the closing itself, the title search, the deed transfer, the settlement statement. What you are describing is a contract and entity problem, not a title problem, so you need a transactional or business attorney who can read both documents at once.
A quick definition of the terms involved. A cross-default provision means that if you default on one loan, your lender on a separate loan can treat that as a default too, even if you are current on their payments. A subordination clause in an operating agreement (the governing document for your LLC) can affect who has priority if the entity's assets are ever claimed. Those two things can interact in ways that affect your lender's collateral position, which is why they flagged it.
As for whether someone dropped the ball: possibly, though I would not say that with certainty before seeing the documents. Six months is a long time for this to surface, and a competent lender review process usually catches entity documents earlier. That said, a cash deal on a new property sometimes triggers a fresh review of your full portfolio, which is when older documents get pulled.
What you need right now is an attorney who can read the operating agreement, the cross-default language, and your existing loan docs together, today if possible, and tell you whether an amendment or a waiver letter resolves it before closing.
A question that would help me give you better context: is your existing lender the same institution as your lender on the two-unit, or are these two completely separate lenders looking at each other's position?