Should have taken borrowers' copy and had them resign correctly and notarize that one - leave them the page that had the mistake.
If company is not happy with how you handled it, it's on you to make them happy. And IMO no, crossing out a signature on your cert and signing yourself over it or above it is not correct. At the least you should have lined through the incorrect cert and attached a clean cert of your own - as Ashton said "a grant dead is one of the most important documents in a package," - you don't mess with that document.
Unfortunately you cut corners and now it's going to end up costing you more time...this correction is on your dime.