Assuming the time limits are in order, of course it can lien your property.
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I am not sure from your question that you and the lender ever had an agreement to lend money. If you do have a loan agreement, it will be spelled out exactly how funds can be disbursed. Normally a lender never does what you say because to do so may invite the lender to be sued for interference. Yes, there can be a lien filed, but your defense will be that the contract was breached due to poor construction. I would take your paperwork from the lender to a lawyer and have it reviewed.
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If you have a loan agreement, that will spell out the lender's obligations regarding disbursement of the loan funds to the contractor and/or to you directly. Regardless of what that agreement provides, the simple answer is that if your contractor performed lien-able services on your home, it can lien for them within 90 days of last furnishing work on the property. If the contractor did not in fact perform the services liened for, or performed them improperly, you can raise that as a defense. You may have other defenses as well. You should have all paperwork regarding the loan and contract with your contractor reviewed by a construction attorney who can advise you on your rights and obligations regarding the lender and contractor.
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