Jean-Louis Akpa Akpro had given the Mariners a 60th-minute opener in the League Two clash but Ryan Lowe stroked home a penalty in the final minute to win a share of the points.
Knill told his club's official website: "There are rumours that he (Scott) is about to join Morecambe. I'd like to know where they come from. I prefer to deal with the truth and the facts.
"We haven't heard anything about Scotty, plus I don't want him to go anywhere. If I did, then he probably wouldn't be here right now.
"Paul Scott has a big part to play and he played a big part on Saturday. I'm delighted with him."